BIS2C_2020. Lecture 7. The Domains of Life.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
BIS2C
Biodiversity & the Tree of Life
Spring 2019
Lecture 7:
The Domains of Life
Prof. Jonathan Eisen

Anna’s Hummingbird in Davis, CA. April 7, 2020
• In previous classes I would leave my screen
saver on with pictures from around UC Davis
and Davis area as people walked into class
•

Learning Goals
1. Understand ways in which the view of the tree of life
has changed over time
2. Understand similarities and differences between
prokaryotic and eukaryotic cell structures
3. Understand the uses of sequence alignments and
comparisons in inferring the structure of the tree of life
4. Compare the structure and implications of the two
current main competing models for the tree of life

!6: The Tree of Life
!7: The Domains of Life
!8: Phylogenetic Diversity of Microbes
Lecture 7 Context

Lecture 7 Outline
• Background and Context
• The Domains of Life
!Introduction
!“Prokaryotes” vs. Eukaryotes
!Three Domain Tree of Life
!Two Domain Tree of Life

Background: Lab Connections
• Lab 2: Tree of life and LUCA
• Lab 1: Classification and the tree of life
• Lab 1: Monophyletic groups and Linnaean
ranks
• Lab 1: Phylogenetic terminology

Background: Review of Lecture 6

Single
Tree?
L6: Tree of Life vs. Trees of Life

Multiple Trees?

Hypothesis 1:
Separate Origins
Hypothesis 2:
Common Origin
Two Hypotheses
How Can We Choose Which
Hypothesis is Best?

List traits found in all organisms.
• 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
• Acquires energy from environment
• Store energy in chemicals
L6: Universal Traits
Yes: not evidence
for common
ancestry.
No: evidence for
common ancestry.
Could trait have
evolved with a
reasonable
probability in
separate origins of
life?

L6: Homology vs. Homoplasy: Ribosome for Translation

• Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
L6: How Do We Study The Origin(s) of Life?
Absolutely no way a separate origin of
life would use the same ribosomes,
with 50+ proteins, multiple rRNAs, and
similar 3D structures and mechanisms

NO WAY: “uses ribosome for translation” could have evolved in
separate origins of life.
Then only possibility is a single tree.
L6: Homology vs. Homoplasy: Ribosome for Translation
Ribosome For Translation

Universal Trait
Trait shared by all organisms.
L6: Universal Homology

Universal Homology
Trait shared by all organisms that could not
have arisen in separate origins of life and
thus is evidence for common ancestry.
L6: Universal Homology

Hypothesis 2:
Common Origin
Hypothesis 1:
Separate Origins
Two Hypotheses
The existence of Universal
Homologies means all life on
Earth is related.

Single Tree
A Single Tree of Life

Now, we care about
the order.
A Single Tree of Life

The Tree of Life

Ernst Haeckel 1866
www.mblwhoilibrary.org
Plantae AnimaliaProtista

Whittaker – Five Kingdoms 1969
Plantae Animalia
Protista
Fungi
Monera

EukaryotesProkaryotes
Chatton 1937 & others: Prokaryotes vs. Eukaryotes

Cell Structure Observations
Prokaryotes vs. Eukaryotes

No Nucleus Nucleus
Two Main Kinds of Structures

No Nucleus Nucleus
What Other Differences Are There?

No Nucleus Nucleus
What Other Differences Are There?
Mitochondria
Endoplasmic
Reticulum
Diploid
MeiosisBinary
Fission
Mitosis
Golgi
Linear DNACircular DNA
Haploid
Chromatin

Interpreted As Implying a Tree

Prokaryotic
Eukaryotic
P1 P2 P3 E1 E2 E3P4
Interpreted as
implying this tree
because this would
require only one event
for the nucleus origin

P1 P2 P3 E1 E2 E3P4
Prokaryotic
Eukaryotic
Interpreted As Implying This Tree Because That Would
Require Only One Event For Nucleus Origin
But this is a mistake
since this tree, also
only requires one
event for origin of
the nucleus

P1 P2 P3 E1 E2 E3P4
Prokaryotic
Eukaryotic
As does this tree

Prokaryotic
Eukaryotic
P1 P2 P3 E1 E2 E3P4
So no reason to
assume this is the
correct tree, even
though many did

• Side lesson — Defining groups based on the
absence of a trait is a bad idea …

Lecture 7 Outline
• Problems with Life v11’s Tree of Life
• The Domains of Life
!Introduction

Three Domain Tree of Life
• There is a better way …

Diversity of Life of Earth

http://mcb.illinois.edu/faculty/profile/1204
1970s - Woese et al.
Carl Woese

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
Woese rRNA Tree of Life

• Skeletons
!All vertebrates have skeletons
!The structure of the skeleton differs between
species and skeletal comparisons can be
used to infer phylogeny
• rRNA
!All organisms have ribosomal RNA
!The sequence of the ribosomal RNA genes
differ between species and sequence
comparisons can be used to infer phylogeny
Woese rRNA Tree of Life vs Skeletons

Prokaryotic
Eukaryotic

Prokaryotic
Eukaryotic
Tree is unrooted.
Why?

Slide from Professor Moore’s Lecture 3

Prokaryotic
Eukaryotic
What is Our
Outgroup?

• Rooted using a special method that is similar
to using an outgroup but is a little different
• Involves using ancient gene duplication
events
Rooting the Tree of Life

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
Rooted Woese rRNA Tree of Life

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
Thought Question
Given this tree, if you group
prokaryotic organisms
together into “prokaryotes”
this group can be described
as:
A: Not monophyletic
B: A clade
C. A natural grouping
D: Prophyletic
E: None of the above

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
Given this tree, if you group
prokaryotic organisms
together into “prokaryotes”
this group can be described
as:
A: Not monophyletic
B: A clade
C. A natural grouping
D: Prophyletic
E: None of the above
Thought Question

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Key Result #1:
“Prokaryotes” Not
Monophyletic
“Prokaryotes” Eukaryotes
Prokaryotic
Eukaryotic

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Key Result #1:
Monophyletic
Prokaryotic
Eukaryotic
We Put Unnatural Groupings in Quotes

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Key Result #1:
Monophyletic
Prokaryotic
Eukaryotic
FOCUS ON
THESE KEY
RESULTS

Prokaryotic G1
P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
Key Result #2:
Two Major Monophyletic
Groups of “Prokaryotes”
Prokaryotic G2

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
Key Result #3:
Three Major
Monophyletic Groups
Rooted Woese rRNA Tree of LifeRooted Woese rRNA Tree of Life
Prokaryotic G1 Prokaryotic G2 Eukaryotes

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
Eukaryotes
Key Result #3:
Three Major
Monophyletic Groups
Prokaryotic G1 Prokaryotic G2

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
New Classification Level?
Key Result #3:
Three Major
Monophyletic Groups
EukaryotesProkaryotic G1 Prokaryotic G2

Domain: ????

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
The Three Domain Tree of Life
The Three Domain
Tree of Life
EukaryotesProkaryotic G1 Prokaryotic G2
The Three Domains

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
EukaryotesEubacteria Prokaryotic G2
Domain 1:
Named “Eubacteria”
(aka “true” bacteria)

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
EukaryotesEubacteria Prokaryotic G2
Domain 2:
What Should We Call It?

Figure 25.16 Some Crenarchaeotes Like It Hot

Figure 25.17 Extreme Halophiles

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
EukaryotesEubacteria Archaebacteria
Domain 2:
Named “Archaebacteria”
(Archae from Greek for
ancient)

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
EukaryotesEubacteria Archaebacteria
BAD BAD Domain 2:
Named “Archaebacteria”
ancient)

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
EukaryotesEubacteria Archaea
Domain 2:
Renamed Archaea
Ancient)

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
Domain 2:
Renamed Archaea
Ancient)
BAD BAD BAD BAD 
BAD BAD BAD BAD

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
Domain 1:
Named “Eubacteria”
(aka “true” bacteria)

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
EukaryotesBacteria Archaea
Domain 1:
Removed the “Eu” part
of the name

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
EukaryaBacteria Archaea
Domain 3:
Named Eukarya

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
EukaryotesBacteria Archaea
Domain 3:
Many Use Eukaryotes

P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
Three Domains

B1 B2 B3 E1 E2 E3B4 A1 A2 A3
Prokaryotic
Eukaryotic
Three Domains
Re-labelled
individual taxa

B1 B2 B3 E1 E2 E3B4 A1 A2 A3
Prokaryotic
Eukaryotic
Key Result #4:
Archaea closer to Eukarya
than to Bacteria

B1 B2 B3 E1 E2 E3B4 A1 A2 A3
Prokaryotic
Eukaryotic
Key Result #4:
Archaea closer to Eukarya
than to Bacteria
Some shared derived traits

Lecture 7 Outline
• Problems with Life v11’s Tree of Life
• The Domains of life
!Introduction

B1 B2 B3 E1 E2 E3B4 A1 A2 A3
Prokaryotic
Eukaryotic
Three Domain Tree of
Life Supported Widely for
Many Year

Loki’s Castle
• Loki’s Castle

Lokiarchaea named after Loki’s Castle Vent Site

B1 B2 B3 E1 E2 E3B4 A1 A2 Loki
Prokaryotic
Eukaryotic
Phylogenetic Trees
Using Genomes from
Lokiarchaea Look Like
This
Alternative to Three Domain Tree of Life

Thorarchaeota
http://sites.utexas.edu/baker-lab/2016/01/29/introducing-thorarchaeota/

B1 B2 B3 E1 E2 E3B4 A1 A2 Loki
Prokaryotic
Eukaryotic
Lokiarchaea and
Thorarchaea Together
in Trees
Thor

Asgard Archaea

B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
A New Clade - The
Asgard Archaea - and
and Alternative Tree of
Life

Asgard Archaea
Something is Wrong Here

Complaining on Twitter …

Response ..

Helarchaeota

Freya not next … Helarchaeota

B1 B2 B3 E1 E2 E3B4 A1 A2 A3
Prokaryotic
Eukaryotic
Three Domain Tree

Prokaryotic
Eukaryotic
New Tree with Asgard
Archaea

• Method developments
!Same data, with different methods,
sometimes gives different results
!Some methods are more prone to artifacts
and errors than others
• Differences between genes
• Better taxonomic sampling
!Can improve resolution in trees
!Can help get around some method problems
Reasons for Changes in the Tree of Life
Two Domain Tree of Life

Prokaryotic
Eukaryotic
How Does This Differ
From The Three
Domain Tree of Life?

Prokaryotic
Eukaryotic
EukaryaBacteria "Archaea”
Key Difference #1:
Archaea not
monophyletic

Prokaryotic
Eukaryotic
EukaryaBacteria “Archaea”
Key Difference #2:
Asgard “Archaea”
Closer to Eukaryotes
than to Other “Archaea”

Prokaryotic
Eukaryotic
EukaryaBacteria "Archaea”
Key Difference #3:
Two Major
Monophyletic Groups

Prokaryotic
Eukaryotic
Bacteria
Renaming The Groups
Archaea

Prokaryotic
Eukaryotic
Bacteria
Archaea

Prokaryotic
Eukaryotic
Bacteria
Archaea
Eukarya
“Prokaryotic
Archaea”

Past, Present and Future
!6: The Tree of Life
!7: The Domains of Life
!8: Phylogenetic Diversity of
Microbes

BIS2C_2020. Lecture 7. The Domains of Life.

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