Microbial Phylogenomics (EVE161) Class 4

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

Phylogeny Review

Internal nodes represent hypothetical ancestral taxa

a b c d e f g h

root, root node

terminal (or tip) taxa

internal nodesinternal

branches

Terminal branches

Parts of a phylogenetic tree

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

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

Data matrices

Sequence Alignment

Tree reconstruction methods

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

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

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

Rooting

Rooting TOL Review

Woese 1987 - rRNA

Microbiological Reviews 51:221

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-TuEF-G

Elongation Factor Evolution

Zoom in ...

EF-Tu EF-G

EF-TuEF-G

Gene duplication event

EF-GEF

EF-Tu EF-G

EF-Tu EF-GGene duplication event

Lecture 7 Outline

• Extracting the gene tree from the species tree

Genes trees in species trees

EF-Tu EF-G

We can extract the gene tree from the species tree

Step 1: Remove species tree

EF-GGene duplication event

Step 2: Untangle gene trees

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

Which taxa are an outgroup to EF-Gs?

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

Which taxa are an outgroup to EF-Tus?

• 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

Alignment of EF-G and EF-Tu

Unrooted tree

Identify different Elongation Factors

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

• Rooting????

Rooting this tree?

Identify different Elongation FactorsE1

Root between the two forms

Identify different Elongation FactorsE1

Trees are equivalent

EF-TuGene duplication event

Outgroup

Bacteria

Archaea

Eukaryotes

OutgroupOutgroup

Outgroup

Bacteria

Archaea

Eukaryotes

Outgroup

Bacteria

Archaea

Eukaryotes

Bacteria

Archaea

Eukaryotes

EF-Tu EF-G

Eukaryotes

Archaea

Bacteria

Homoplasy

Bootstrapping

Jacknifing

Congruence

Masking

Concatenation

Microbial Phylogenomics (EVE161) Class 4

Science

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