BiS2C: Lecture 8: The Tree of Life II

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Lecture 8:
The Tree of Life:II
BIS 002C
Biodiversity & the Tree of Life
Spring 2016
Prof. Jonathan Eisen
1

Where we are going and where we have been
• Previous Lecture:
!7: The Tree of Life I
• Current Lecture:
!8: The Tree of Life II
• Next Lecture:
!9: Culture
2

Thought Questions & Main Topics
• How can the Tree of Life be rooted?
• What is the overall structure of the Tree of
Life?
• How can we use this structure to better
understand life?
• What diversity (form, function, phylogeny)
is there within each Domain?
3

Key Concepts
• Rooting, ingroups and outgroups
• Domains and Classification
• Characters: states, ancestral, derived
• Gene trees & species trees
• Competing Trees of Life
• Office Hours today 4-5 pm in 3089 SLB
(CLC)
4

5
Life?
understand life?

Woese Tree of Life
6
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
Eubacteria
Archaebacteria

Unrooted Tree of Life from Woese
7

Simplified Three Domain Unrooted Tree of Life
8
Eukaryotes
Archaea Bacteria

Table 26.1: Features of the Three Domains of Life
9

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 10
TEST HINT: STUDY THESE
Table 26.1: Features of the Three Domains of Life

11
Eukaryotes
Archaea Bacteria

12
Eukaryotes
Archaea Bacteria
D Domain
K Kingdom
P Phylum
C Class
O Order
F Family
G Genus
S Species

Unrooted Tree of Three Primates
19
Humans
Chimps Gorilla

Resolving the Primate HCG Polytomy
Humans GorillasChimps

Outgroup for the Tree of Life?
Humans GorillasChimpsOrangutans

Unrooted Tree of Three Primates w/ Outgroup
23
H
C
O
G
H
O
C
G
H
G
O
C

Which of these Trees is Unique Compared to the Others
26
H
C
O
G
G
O
H
C
C
G
O
H
H
O
C
G
G
H
O
C
C
G
H
O
1
2
3 6
5
4
A: 1
B: 3
C: 4
D: 5
E: none

Unrooted Tree of Three Primates w/ Outgroup
29
H
C
O
G
H
O
C
G
H
G
O
C
H GCO

30
Eukaryotes
Archaea Bacteria

Outgroup
Bacteria Archaea Eukaryotes

Outgroup for the Tree of Life
INGROUP
OUTGROUP

Lots of Genes Within Each Species / Lineage

Lots of Genes Within Each Species / Lineage
Gene Trees & Species Trees
Genes Within Genomes Have
An Evolutionary History Too
This Can Be Represented by a
Phylogenetic Tree

If Species Tree has AE Group, So Should Gene Tree

If Species Tree Has AB Group So Should Gene Tree

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
INGROUP
OUTGROUP
Gene Duplications Prior to MRCA of All Life
Sandra
Baldauf

Semi-resolved Phylogeny of Elongation Factors
EF-TU
EFG

If AB Together Should Be For Both EF2 and EFG
EF-TU
EFG

If AE Together Should Be For Both EF2 and EFG
EF-TU
EFG

43
Life?
understand life?

A
B
E
EFG
A
E
B
EFG
E
B
A
EFG
EFG
Rooted Tree of 3 Domains from EFTu (EFG Outgroup)
EF-Tu

Unrooted Tree of 3 Domains from EFG (EFTu Outgroup)
49
A
B
E
EFTu
A
E
B
EFTu
E
B
A
EFTu
EFTu
EF-G

Phylogenetic Tree of Elongation Factors
EF-TU
EFG

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
INGROUP
OUTGROUP
Gene Duplications Prior to MRCA of All Life
Sandra
Baldauf

Elongation Factor Rooting
52

Winner
Three Domain Tree of Life

Prokaryotes
55
Paraphyletic
Rooted Three Domain Tree of Life

56

57
ROOT

Rooted Three Domain Tree of Life

59
ROOT
MAJOR DEBATE/AMBIGUITIES

Alternative Position of Eukaryote Branch
60
ROOT

Eocyte Tree
New Winner
(maybe)

Eocyte Tree
TACK
New Winner
(maybe)

Loki
65

66
Life?
understand life?

Implications of the Rooted Tree of Life

Similar to Implications of This Tree

Table 26.1
69

Evolution of Traits on a Tree
• Tracing the Evolution of Traits and States
• NOT using these characters to infer the branching
patterns.
• Branching patterns and rooting inferred from molecular
sequence data.
• Many of these characters would NOT be informative to
infer the phylogenetic relationships among the groups
70

Unique Bacterial Features
71

Unique Bacterial Features
Cell envelope
of bacteria
contains
peptidoglycan
- a special
polymer of
amino sugars.
Not seen in
Archaea or
Eukaryotes

Peptidoglycan
Has peptidoglycan
No peptidoglycan

Unique Archaeal Features
75

Archaeal Membranes
Ester
Ether
Read Ch 26 on the
differences in
membranes

Ester
Ether
Archaeal Membranes

Eocyte Tree
TACK
New Winner
(maybe)

Eocyte Tree
TACK
Ester
Ether

Unique Eukaryotic Features

Nucleus
82

N N
N Has nucleus
No nucleus
Evolution of the Nucleus

N N
N
N Has nucleus
No nucleus
Evolution of the Nucleus
Gain of nucleus

Transcription and Translation in Eukaryotes
85
• Transcription by multiple 
RNA polymerases
• Complex promoter and
enhancer structures
• Extensive splicing of RNA
• Introns and Exons
• Export of RNA out of
nucleus
• Translation in cytoplasm

Figure 9.19 Mitosis
86

Meiosis
87

Mitochondria
88

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
89

Eukaryotes are Different …
Many gains

Features Shared by Bacteria and Archaea
++ ++ ++ ++

Binary Fission
92

++ ++ ++ ++
Evolution of Binary Fission
No binary fission
Has binary fission++
++ ++
++
++
Loss of binary
fission

Evolution of Eukaryotes
Many losses
here too

WHAT
HAPPENED
HERE?
Eukaryotes are Different …

Eocyte Tree
SEARCH
FOR THESE
TACK

Histones (for chromosome coiling)
TACK
- - - -

98
Life?
understand life?

Figure 26.1 The Three Domains of the Living World
Low-GC Gram-positives
Origin of
mitochondria
ARCHAEA
EUKARYA
BACTERIA
Origin of
chloroplasts
Origin of
life
Euryarchaeota
Crenarchaeota
All eukaryote phyla
Proteo-
bacteria
Chlamydias
Spirochetes
Cyanobacteria
Hadobacteria
Hyperthermophilic bacteria
High-GC Gram-positives

Figure 27.3 Precambrian Divergence of Major Eukaryote Groups

Diversity Within Each Domain

Tack

Gram stains

Gram stains
• The gram stain method reveals two different
types of bacterial cell walls.
• Gram-positive bacteria have a thick layer of
peptidoglycan outside the plasma membrane.
• Gram-negative bacteria have a thin layer of
peptidoglycan between the plasma membrane
and another distinct outer membrane, in the
periplasmic space.
• Antibiotics such as penicillin interfere with the
synthesis of the cell walls, but don’t affect
eukaryote cells.
105

Extreme Halophiles
106

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