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

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

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

• Brad Pitt movie

• Natural food remedies

• Art by the arboretum

• Name of my blog

Tree of Life Imagery is Everywhere

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?

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

Life on Mars

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

Life on Mars

Are These Separate Trees or Connected?

Life on EarthLife on Mars

Evidence?

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

• (Assuming of course that Donald Trump is alive)

Not Just A Thought Experiment

Dawn Sumner - UC Davis Geology Professor

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

Diversity of Life

Darwin - Tree or maybe Trees of Life

“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

Life on EarthLife on Earth

Multiple Origins of Life on Earth

Single Origin of Life on Earth

Single Origin of Life on Earth EVIDENCE????

Diversity of Life

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

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

! 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

Universal Homologies

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

Central Dogma in All Organisms

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

Figure 14.14 Ribosome Structure

• Historical Trees of Life

The Tree of Life

Ernst Haeckel 1866

34www.mblwhoilibrary.org

Plantae AnimaliaProtista

Whittaker – Five Kingdoms 1969

Plantae Animalia

Protista

Monera

Prokaryotes vs. Eukaryotes

EukaryotesProkaryotes

Limitations of This?

• Are all prokaryotes the same?

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

Possible Trees

Tree 1

Prok Euk

Tree 2

Alternative Trees

Prok Euk

Tree 3

Alternative Trees

Prok Euk

Tree 4

Alternative Trees

Prok Euk

Clicker

Which Tree is Most Parsimonious (character: nucleus)?

Tree 1 Tree 2

Tree 3 Tree 4

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

Tree 1 Tree 2

Tree 3 Tree 4

Which Tree is Most Parsimonious (character: nucleus)?

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

Which Tree is Most Parsimonious?

Tree 1 Tree 2

Tree 3 Tree 4

How many character state changes needed?

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

In Which Tree are Prokaryotes Monophyletic

Tree 1 Tree 2

Tree 3 Tree 4

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

In Which Tree are Prokaryotes Monophyletic?

Tree 1 Tree 2

Tree 3 Tree 4

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

In Which Tree are Prokaryotes Monophyletic?

Tree 1 Tree 2

Monophyletic Group = Clade

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

In Which Tree are Eukaryotes Monophyletic

Tree 1 Tree 2

Tree 3 Tree 4

Conclusion

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

• Historical Trees of Life

• The Modern Tree of Life

Diversity of Life

Carl Woese

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

Woese Tree of Life

rRNA rRNArRNA

Woese Tree of Life

rRNA rRNArRNA

Woese Tree of Life

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

Woese Tree of Life

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

Woese Tree of Life

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

Taxa Characters S ACUGCACCUAUCGUUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

Woese Tree of Life

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

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

Woese Tree of Life

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

Woese Tree of Life

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

Woese Tree of Life

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

Woese Tree of Life

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

Eukaryotes

Woese Tree of Life

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

EukaryotesEubacteria

Woese Tree of Life

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

Woese Tree of Life

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

Woese Tree of Life

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

Woese Tree of Life

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

Archaebacteria

Unrooted Tree of Life from Woese

Simplified Three Domain Unrooted Tree of Life

Eukaryotes

Archaebacteria Eubacteria

Archaea Dominate Extremely Hot Environments

Archaea Dominate Extremely Salty Environments

Table 26.1 The Three Domains of Life on Earth

Eukaryotes

Archaebacteria Eubacteria

Eukaryotes

Archaea Eubacteria

Eukaryotes

Archaea Bacteria

Eukaryotes

Archaea Bacteria

Eukaryotes

Archaea Bacteria

Can You Tell Which Groups are Sister Taxa from this?

Eukaryotes

Archaea Bacteria

What is Missing?

Clicker

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

B: 1 C: 2 D: 3

E: Not possible to determine

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

Eukaryotes

Archaea Bacteria

Eukaryotes

Archaea Bacteria

Eukaryotes

BacteriaArchaea

Eukaryotes

BacteriaArchaea

Eukaryotes

BacteriaArchaea

Eukaryotes

BacteriaArchaea

Eukaryotes

BacteriaArchaea

Eukaryotes

Bacteria

Eukaryotes

Bacteria

Archaea

Eukaryotes

Bacteria

Archaea

Eukaryotes

Bacteria

Archaea

Eukaryotes

Bacteria

Archaea

Eukaryotes

Bacteria

Archaea

Bacteria

Archaea

Bacteria

Archaea Eukaryotes

Bacteria

Archaea Eukaryotes

Bacteria

Archaea Eukaryotes

Archaea BacteriaEukaryotes

Eukaryotes

Archaea Bacteria

Eukaryotes

Archaea Bacteria

Eukaryotes

Archaea Bacteria

A Polytomous Three Domain Tree of Life

Bacteria Archaea Eukaryotes

Polytomy

Clicker Question

Clicker

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

Bacteria EukaryotesArchaea

Clicker

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

Eukaryotes and Archaea as Sister Groups

EukaryotesBacteria

Bacteria

Eukaryotes and Bacteria as Sister Groups

EukaryotesArchaea

Resolving the Tree of Life Polytomy

Bacteria EukaryotesArchaea

Phylogenetic Inference

polytomy

outgroup

Outgroup

Outgroup for the Tree of Life?

BiS2C: Lecture 7: The Tree of Life

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