Lecture 3:

EVE 161:Microbial Phylogenomics

Lecture #4: Background on Phylogeny

UC Davis, Winter 2016 Instructors: Jonathan Eisen & Holly Ganz

Where we are going and where we have been

• Previous lecture: !3. Woese and the Tree of Life

• Current Lecture: !4. Background on Phylogeny

• Next Lecture: !5. Modern view of Tree of Life

!2

Phylogeny Review

!3

Internal nodes represent hypothetical ancestral taxa

a b c d e f g h

root, root node

terminal (or tip) taxa

internal nodesinternal

branches

u

v

wx

yz

t

Terminal branches

Parts of a phylogenetic tree

!4

Characters

• A heritable feature of an organism is known as a character (also character trait or trait).

• The form that a character takes is known as its state (also known as character state). ! Note: Presence/absence can be a state

• Example: ! Character = heart ! Character state = present/absent ! Character state = # of chambers

!5

Characters ancestry is critical to understand

• Characters that are inherited from a common ancestor are homologous.

• Species change over time ! Known (generally) as divergence, or divergent

evolution. ! Species change over time due to the combined

processes of mutation, recombination, drift, selection, etc

!6

Data matrices

!7

Sequence Alignment

8

Tree reconstruction methods

!9

UPGMA

Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm

The True Tree

Distance Matrix For True Tree

Collapse Diagonal

Identify Lowest D

OTUs A B C D E

B 2

C 4 4

D 6 6 6

E 6 6 6 4

F 8 8 8 8 8

Join Those Two Taxa

• Create branch with length = D

• 2• A--------------B

Make D from Node Equal

Create New Distance Matrix

• Merge Two OTUs joined in previous step (AB)

• Dx, AB = 0.5 * (Dx, A + Dx, B)

New Matrix

UPGMA

Compare to True Tree

But …

• What is evolutionary rates not equal

Unequal rates

UPGMA with Unequal rates

Compare to True Tree

Likelihood

• Based on Bayes’ Theorem• Prob(H|D) = Prob(H and D) ÷ Prob(D)

• Prob(H|D) = Prob(D|H) x Prob(H) ÷ Prob(D)

Bayesian

• Based on Bayes’ Theorem• Prob(H|D) = Prob(H and D) ÷ Prob(D)

• Prob(H|D) = Prob(D|H) x Prob(H) ÷ Prob(D)

Long branch attraction

!28

Rooting

!29

Rooting TOL Review

Woese 1987 - rRNA

Microbiological Reviews 51:221

Woese

The Tree of Life2006

adapted from Baldauf, et al., in Assembling the Tree of Life, 2004

The Tree of Life2006

adapted from Baldauf, et al., in Assembling the Tree of Life, 2004

Simplified, Rooted Tree of Life

TTwo different kinds of elongation factors

Elongation Factor Tu (EF-Tu)

Elongation Factor G (EF-G)From Steitz Nature Reviews MCB 9: 242. 2008

Translation

TTwo different kinds of elongation factors in all organisms

Who has two EFs?

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

MRCA

EF-TuEF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

Elongation Factor Evolution

Zoom in ...

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

MRCA

EF-TuEF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF

Gene duplication event

Elongation Factor Evolution

MRCA

Gene duplication event

EF-Tu

EF-GEF

EF-Tu

EF-G

EF-Tu

EF-G

Elongation Factor Evolution

MRCA

Gene duplication event

EF-Tu

EF-GEF

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

Elongation Factor Evolution

MRCA

Gene duplication event

EF-Tu

EF-GEF

EF-Tu

EF-Tu

EF-Tu

EF-G

EF-G

EF-G

Elongation Factor Evolution

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-GGene duplication event

EF

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

EF-Tu

EF-G

Elongation Factor Evolution

Lecture 7 Outline

• Extracting the gene tree from the species tree

Genes trees in species trees

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-GGene duplication event

EF

We can extract the gene tree from the species tree

Step 1: Remove species tree

Elongation Factor Evolution

EF-G

EF-G

EF-G

EF-G

EF-G

EF-G

EF-G

EF-GGene duplication event

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF

We can extract the gene tree from the species tree

Step 2: Untangle gene trees

Elongation Factor Evolution

EF-G

Gene duplication event

EF-Tu

EF

We can extract the gene tree from the species tree

Step 2: Untangle gene trees

1

2

3

4

56

7

8

1

2

3

4

56

7

8

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-G

EF-G

EF-G

EF-G

EF-G

EF-G

EF-G

Elongation Factor Evolution

EF-G

Gene duplication event

EF-Tu

EF 1

2

3

4

56

7

8

1

2

3

4

56

7

8

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-G

EF-G

EF-G

EF-G

EF-G

EF-G

EF-G

Any/all EF-TUs are Outgroup of EF-Gs

Which taxa are an outgroup to EF-Gs?

Elongation Factor Evolution

EF-G

Gene duplication event

EF-Tu

EF 1

2

3

4

56

7

8

1

2

3

4

56

7

8

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-Tu

EF-G

EF-G

EF-G

EF-G

EF-G

EF-G

EF-G

Any/all EF-Gs are Outgroup of EF-TUs

Which taxa are an outgroup to EF-Tus?

Elongation Factor Evolution

• For 9 species ! Three archaea (A1, A2, A3) ! Three eukaryotes (E1, E2, E3) ! Three bacteria (B1, B2, B3)

• Take their EF-TU and EF-G genes

• Align them to each other ! This is your data matrix !Note - there are lots of phylogenetically

informative positions in the alignment

• Build unrooted tree

Elongation Factor Evolution

Alignment of EF-G and EF-Tu

Elongation Factor Evolution

E1

E2

E3

B3

B1

B2

A1

A3

A2E1

E2

E3

B3

B1

B2

A1

A3A2

Unrooted tree

Elongation Factor Evolution

Identify different Elongation Factors

E2

E3

B3

B1

B2

A1

A3

A2

E1

E1

E2

E3

B3

B1

B2

A1

A3A2

EF-Tu

EF-G

Each species has one of each EF-G and EF-Tu

Elongation Factor Evolution

• Rooting????

Rooting this tree?

Identify different Elongation FactorsE1

E2

E3

B3

B1

B2

A1

A3

A2E1

E2

E3

B3

B1

B2

A1

A3A2

EF-Tu

EF-G

Root between the two forms

Elongation Factor Evolution

Identify different Elongation FactorsE1

E2

E3

B3

B1

B2

A1

A3

A2

E1

E2

E3

B3

B1

B2

A1

A3

A2

EF-Tu

EF-G1

2

3

E

E

E

A

A

A

B

B

B

E

E

E

A

A

A

B

B

B

EF-G

EF-Tu

1

2

3

4 45

5

6

6

Trees are equivalent

Elongation Factor Evolution

E1

E2E3

A1

A2

A3

B1

B3

B2

E1

E2E3

A1

A2

A3

B1

B3

B2

EF-G

EF-TuGene duplication event

Elongation Factor Evolution

E1

E2E3

A1

A2

A3

B1

B3

B2

E1

E2E3

A1

A2

A3

B1

B3

B2

EF-G

EF-TuGene duplication event

Outgroup

Elongation Factor Evolution

E1

E2E3

A1

A2

A3

B1

B3

B2

E1

E2E3

A1

A2

A3

B1

B3

B2

EF-G

EF-TuGene duplication event

Outgroup

Bacteria

Archaea

Eukaryotes

Elongation Factor Evolution

E1

E2E3

A1

A2

A3

B1

B3

B2

E1

E2E3

A1

A2

A3

B1

B3

B2

EF-G

EF-TuGene duplication event

OutgroupOutgroup

Elongation Factor Evolution

E1

E2E3

A1

A2

A3

B1

B3

B2

E1

E2E3

A1

A2

A3

B1

B3

B2

EF-G

EF-TuGene duplication event

Outgroup

Bacteria

Archaea

Eukaryotes

Outgroup

Elongation Factor Evolution

E1

E2E3

A1

A2

A3

B1

B3

B2

E1

E2E3

A1

A2

A3

B1

B3

B2

EF-G

EF-TuGene duplication event

Bacteria

Archaea

Eukaryotes

Bacteria

Archaea

Eukaryotes

Elongation Factor Evolution

Elongation Factor Evolution

EF-Tu EF-G

EF-Tu EF-G

EF-Tu EF-GGene duplication event

EF

Eukaryotes

Archaea

Bacteria

Elongation Factor Evolution

Homoplasy

!64

Bootstrapping

!65

Jacknifing

!66

Congruence

!67

Masking

!68

Concatenation

!69