BIS2C. Biodiversity and the Tree of Life. 2014. L5. The Tree of Life

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Lecture 5

!

Lecture 5 & 6: !

The Tree of Life !!!

BIS 002C Biodiversity & the Tree of Life

Spring 2014 !

Prof. Jonathan Eisen

1


• Brad Pitt movie

• Natural food remedies

• Art by the arboretum

• Name of my blog

!2

Tree of Life Imagery is Everywhere

2


Where we are going and where we have been

• Previous Lecture: !4: Inferring Trees

• Current Lecture: !5: The Tree of Life

• Next Lecture: !6: The Tree of Life

3


Lecture 5 & 6: Outline

• Lecture 4 Wrap Up

• Lecture 5-6: The Tree of Life

4


Lecture 4: Phylogenetic Inference

• General issues

• Case study

• Parsimony inference for case study

• Parsimony informativeness

• Character conflict

• Are all changes equal?

5


! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa!Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! ! ! 1 ! Tree 2!! ! ! 2! Tree 3!! ! ! 2

A A GG A G AG A G AG

Tree 1 Tree 2 Tree 3

GA

G GA

A

GA

A


! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa!Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! ! ! ! ! ! 1 ! Tree 2!! ! ! ! ! ! 2! Tree 3!! ! ! ! ! ! 2

T T CC T C TC T C TC


CT

C CT

T

CT

T


! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa!Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! ! ! ! ! ! ! 2! Tree 2!! ! ! ! ! ! ! 1! Tree 3!! ! ! ! ! ! ! 2

A C AC C A AC C A AC

Tree 1 Tree 2 Tree 3CC

CC

A

CC

CC


Character Conflict

• Character conflict is expected and routine

• Sometimes it is just “noise”

• Sometimes it reflects convergent evolution

• Sometimes it is due to more complex histories (stay tuned)

9


Lecture 4: Phylogenetic Inference

• General issues

• Case study

• Parsimony inference for case study

• Parsimony informativeness

• Character conflict

• Are all changes equal?

10


Key Concept: Not all Changes Occur at the Same Rate

11


A G

T C

Transitions and transversions

12


Pyrimidines

Purines

A G

T C


13


Pyrimidines

Purines

A G

T C


14

Transition

Transition


Transversion

Pyrimidines

Purines

A G

T C


15

Transition

Transition


! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa!Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1!0!1!1!2!0!1!4!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!5! Tree 3!! 1!0!2!0!1!2!2!0!1!6

H C GO C G HO C G HO


Transitions?

Transversions?





Transitions?

Transversions?




Transitions?

Transversions?





Transitions?

Transversions?





Transitions?

Transversions?





Transitions?

Transversions?





Transitions?

Transversions?





Transitions?

Transversions?





Transitions?

Transversions?





Transitions?

Transversions?





Transitions?

Transversions?





Transitions?

Transversions?





Transitions?

Transversions?





Transitions?

Transversions?





Transitions?

Transversions?



• In inferring which tree is the “best tree” what if we counted transitions differently than transversions?

!

• Why might we do this?

19




Transitions?

Transversions?






Transitions?

Transversions?





Transitions?

Transversions?

Tv = 2 x Ts





Transitions?

Transversions?

Tv = 2 x Ts





Transitions?

Transversions?

Tv = 2 x Ts





Transitions?

Transversions?

Tv = 3 x Ts





Transitions?

Transversions?

Tv = 3 x Ts





Transitions?

Transversions?

Tv = 3 x Ts





Transitions?

Transversions?

Tv = 3 x Ts

Tree 2 does better because it only requires one rare event.


Clicker

29


Clicker

How many characters show transition differences?

30

! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa!Orang! ! C!T!G!G!A!G!C!C!G! Chimp! ! C!T!A!G!C!G!C!C!A! Gorilla! T!T!G!G!C!G!A!C!A! Human! ! T!T!A!G!C!G!A!C!G

A: 1 B: 2 C: 3 D: 4


Clicker

How many characters show transition differences?

31

! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa!Orang! ! C!T!G!G!A!G!C!C!G! Chimp! ! C!T!A!G!C!G!C!C!A! Gorilla! T!T!G!G!C!G!A!C!A! Human! ! T!T!A!G!C!G!A!C!G

A: 1 B: 2 C: 3 D: 4


Some Assumptions

• All types of characters are equivalent

• All types of changes are equivalent

• Changes on all branches equivalent

32


Cladograms vs. Phylograms

33

A

C

BD

A CB D

Branch length is proportional to the amount of character change

Phylogram

No meaning to branch lengths.

Cladogram


Assumption III

• Why might some branches be different from others?

• Rates of evolution are not uniform. Some lineages (e.g., HIV) evolve more rapidly than others (e.g., humans)

34


Key Concept: Likelihood methods

• Compare different trees and give each a score

• Rather than searching for trees with the fewest changes, likelihood based methods assign trees probabilities

• The probabilities that are calculated do not favor one reconstruction 100% over others

• They are based on a probabilistic model of evolution of characters.

• Longer branches have higher probabilities of changes occurring on them

• Probabilities of different types of changes can be accounted for readily

35


Lectures 5-6: Outline

• Universal homologies

• Past attempts at the tree of life

• The three domain tree

• Relationships among domains

• Implications of rooted tree of life

• Viruses

• Complications

36








• Viruses

• Complications

37


Diversity of Life

38


Phylogeny Is Critical to Understanding Diversity

39


Diversity of Life

40


Diversity of Life

41

Morphology?

Physiology?

Behavior?


Diversity of Life

42


Central Dogma in All Organisms

43

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

44


Figure 14.14 Ribosome Structure

45


Key Concept: Universal homologies

Universal homologies are characters found

• in all organisms

• to be homologous (i.e., similarity is due to common ancestry)

46


Universal homologies - implications

Key implication of the existence of universal homologies?

!

• All life is related

• And thus can view the interconnectedness of organisms as “The Tree of Life”

47


Clicker

48


Clicker

The patterns of presence and absence of universal homologies in taxa cannot be used to infer the phylogenetic relationships among organisms? • A. True • B. False

49


Clicker

The patterns of presence and absence of universal homologies in taxa cannot be used to infer the phylogenetic relationships among organisms? • A. True • B. False

50


Universal homologies

51

Organism DNA Three letter code

DNA-> RNA-> protein

E. coli (bacteria) + + +

S. cerevisieae (eukaryote) + + +

H. sapiens (eukaryote) + + +

M. jannaschii (archaea) + + +


Tree 1

a b c d e h g f

52


Tree 2

a b c d e h g f

53








• Viruses

• Complications

54


Ernst Haeckel 1866

55www.mblwhoilibrary.org


Ernst Haeckel 1866


Animalia


Ernst Haeckel 1866


Plantae Animalia


Ernst Haeckel 1866


Plantae AnimaliaProtista


Whittaker – Five Kingdoms 1969

56



56

Animalia



56

Plantae Animalia



56

Plantae Animalia

Protista



56

Plantae Animalia

Protista

Fungi



56

Plantae Animalia

Protista

Fungi

Monera


Appearance not Useful

57


Prokaryotes (Bacteria) vs. Eukaryotes

58

EukaryotesProkaryotes



59

Bacteria Eukaryotes



60

Bacteria Eukaryotes



61

Bacteria Eukaryotes



62








• Viruses

• Complications

63


Diversity of Life

64


Woese Tree of Life

65


Woese Tree of Life

65


Woese Tree of Life

65


Woese Tree of Life

65


Woese Tree of Life

65


Woese Tree of Life

65

rRNA rRNArRNA


Woese Tree of Life

65

rRNA rRNArRNA


Woese Tree of Life

65

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG


Woese Tree of Life

65

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG


Woese Tree of Life

65

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG


Woese Tree of Life

65

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



Woese Tree of Life

65

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG




Woese Tree of Life

65

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG




Woese Tree of Life

65

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG




Woese Tree of Life

65

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG




Woese Tree of Life

65

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG



Eukaryotes


Woese Tree of Life

65

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG



EukaryotesBacteria


Woese Tree of Life

65

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG



EukaryotesBacteria ?????


Woese Tree of Life

65

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG



EukaryotesBacteria ?????Archaebacteria


Three Domains of Life

66

Bacteria Archaebacteria Eukaryotes


Unrooted Tree of Life from Woese

67



68

Bacteria Archaebacteria Eukaryotes


Archaea Dominate Extremely Hot Environments

69


Archaea Dominate Extremely Salty Environments

70



71

Bacteria Archaea Eukaryotes


Table 26.1 The Three Domains of Life on Earth

72








• Viruses

• Complications

73


Clicker Question

74



75


Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 76


Clicker Question How Many Distinct Ways To Resolve this Polytomy? A: 2 B: 3 C: 4 D: 5



Clicker Question How Many Distinct Ways To Resolve this Polytomy? A: 2 B: 3 C: 4 D: 5



Archaea and Bacteria as Sister Groups


Bacteria ArchaeaEukaryotes

Eukaryotes and Bacteria as Sister Groups



Archaea and Eukaryotes as Sister Groups


Resolving the Tree of Life Polytomy

81


Phylogenetic Inference

polytomy


polytomy

outgroup

Phylogenetic Inference



Outgroup for the Tree of Life?

Outgroup



























EF




EF




EF

EF-G EF-Tu




EF

EF-G EF-Tu




EF

EF-G EF-Tu




EF

EF-G EF-Tu

Taxa Characters! B1 EFG ACUGCACCUAUCGUUCG! B2 EFG ACUCCACCUAUCGUUCG! E1 EFG ACUCCAGCUAUCGAUCG! E2 EFG ACUCCAGGUAUCGAUCG! A1 EFG ACCCCAGCUCUCGCUCG! A2 EFG ACCCCAGCUCUGGCUCG! B1 EF2 ACAACAGCUCUGACUGG! E1 EF2 CCAACAGCUCUGACUGG! A1 EF2 ACAACAGUUUUGACUGG




EF

EF-G EF-Tu


INGROUP




EF

EF-G EF-Tu


INGROUP

OUTGROUP




Winner



Rooted Tree of Life

Winner !

Sort of …



Eocyte Tree



Winner

Rooted Tree of Life








• Viruses

• Complications

93


Clicker



Given this tree, prokaryotes can be described as: !A: Paraphyletic B: Monophyletic C: Quasiphyletic D: Multiphyletic



Prokaryotes are Paraphyletic

Given this tree, prokaryotes can be described as: !A: Paraphyletic B: Monophyletic C: Quasiphyletic D: Multiphyletic


Prokaryotes

97


Prokaryotes are Paraphyletic

Paraphyletic


Unique Archaeal Features

98



Archaeal Membranes

Ester

Ether



Ester

Ether

Archaeal Membranes


Unique Bacterial Features

101


Unique Bacterial Features

102

Outside of cell

Outside of cell

Inside of cell

Inside of cell

Cell envelope

Cell wall (peptidoglycan)

Plasma membrane

Outer membrane of cell envelope

Periplasmic space

Peptidoglycan layer

Periplasmic space

Plasma membrane

5 µm

5 µm

Cell envelope of bacteria contains peptidoglycan, special polymer of amino sugars. !Not seen in Archaea or Eukaryotes



Peptidoglycan

Has peptidoglycan

No peptidoglycan



Peptidoglycan

Has peptidoglycan

No peptidoglycan


Clicker

105



Using parsimony reconstruction, what can you infer about the ancestral character state?

!A: Ancestral state = has peptidoglycan B: Ancestral state = does not have peptidoglycan C: Cannot tell



Using parsimony reconstruction, what can you infer about the ancestral character state?

!A: Ancestral state = has peptidoglycan B: Ancestral state = does not have peptidoglycan C: Cannot tell



Model 1

Has peptidoglycan

No peptidoglycan



Model 2

Has peptidoglycan

No peptidoglycan


Unique Eukaryotic Features

110


Nucleus

111



Evolution of the Nucleus



N N

N Has nucleus

No nucleus




N N

N Has nucleus

No nucleus




N N

N

N Has nucleus

No nucleus




Evolution of Eukaryotes

Lots of things gained and lost here


Figure 14.7 Transcription of a Eukaryotic Gene

117


Figure 9.19 Mitosis

AnaphaseParent cell (2n)

Prophase Metaphase Two daughter cells (each 2n)

2n 2n

118


Meiosis

119


Fig 8-33 Telomerase carries a short RNA molecule that acts as a template for the addition of the complementary DNA sequence at the 3’ end of the double helix. In the ciliate Tetrahymena, the DNA sequence added is TTGGGG

Telomeres

120


Figure 9.2 Bacterial and Archaeal Cell Division (Part 1)

Plasma membrane

Chromosome

121


Conjugation

122






Prokaryotes

124






WHAT HAPPENED

HERE?

Eukaryotes are Different …



STAY TUNED









• Viruses

• Complications

127


Complication #1: Eukaryotes

128


Eukaryote genome

129

Chromosome

Centromere sequences

Telomere sequences

Promoter containing regulatory sequences

mRNA

mRNA polymerase

Open reading frame (protein-coding sequence: exons)

Terminator of transcription

tRNA gene rRNA genes

tRNA

RibosomesTransposons




For Part of the Eukaryotic

Genome the Tree Looks Like This




For other parts it looks like this

Bacteria


Different histories within one genome

132


Bacteria ArchaeaEukaryotes Bacteria

Three Domain Tree

Alternative Tree



132



Three Domain Tree

Alternative Tree



132



Three Domain Tree

Alternative Tree


Chimeras

133


Mitochondria

134


Mitochondria

135

Many similarities to bacteria / archaea


Appearance not Useful

136


Mitochondria

137

Many similarities to bacteria / archaeaDNA


An ancestor of eukaryotes

138

Cell membrane

Genome


αProteo

Genome

Bacterial cell envelope

Cell membrane

Genome

A symbiosis with a proteobacterium


Engulfment

140

αProteo

Cell membrane

Genome

Genome



αProteoCell membrane

Genome

Genome


Host membrane

Endosymbiosis


Origin of the nucleus

142

N

αProteo

Host membrane

Nucleus

Cell membrane

Genome

Genome



Mitochondria

143

N

Mitochondrion

Genome

MNucleus

Cell membrane

Genome




For Part of the Eukaryotic

Genome the Tree Looks Like This




For other parts it looks like this

Bacteria


Early eukaryotes

146

N

Mitochondrion

Genome

MNucleus

Cell membrane

Genome


Lateral gene transfer to the nucleus

147

N

Mitochondrion

Genome

MNucleus

Cell membrane

Genome


Chimeric eukaryotes

148



Three Domain Tree

Alternative Tree


Chimeric eukaryotes

148



Three Domain Tree

Alternative Tree


Chimeric eukaryotes

148



Three Domain Tree

Alternative Tree

Science

BIS2C. Biodiversity and the Tree of Life. 2014. L5. The Tree of Life