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






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

EukaryotesEubacteria

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

4A: 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






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

EFTuBacteria Archaea Eukaryotes

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

ROOTMAJOR DEBATE/AMBIGUITIES


Alternative Position of Eukaryote Branch

60

ROOT



Eocyte Tree

New Winner (maybe)



Eocyte Tree

TACK

New Winner (maybe)


Loki

65



66







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 multipleRNA 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





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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