Viral Evolution and Recombination

Peter Norbergpeter.norberg@gu.se

Phylogenetic analysis

• Reconstruction of

evolutionary history

• Relationship

• Distance

• Common ancestors

Tree of Life

Viruses and Viral Evolution

• Viruses are not living organisms!

• but evolving…

• Genetic material (DNA or RNA)

• Need to adapt to their environment!

Different representations of phylogenetic trees

A B C D

ABCD

AB

C

D

A

BC

D

ABCD

Bootstrap

-A way to get “statistical significance” of a certain topology

-Construct several new sequence sets (1000 st.)

-A new sequence set is generated by randomly picking of columns from the original set

-Apply the phylogenetic algorithm on all sets.

-Make one consensus tree from all trees

BootstrappingA: AACTTAACCACGCTATCGATGCAATTATATAB: AATTTGACTGCGGTACCGATCCAATTATATAC: AATTTGACTGGGCTACCGATCCAATTATATAD: AACTTAACCGCGCTACTGATCGAATTATATA

A: CACCB: TGCTC: TGCTD: CAGC

A

D

B

C

96

96

A

B

C

D

3

3

A

C

B

D

1

1

Recombination

• A powerful genetic mechanism

• Used by all animals (extremely few exceptions)

• Beneficial despite “the cost of sex”

• Speeds up evolution (up to 10,000 times)

• Accumulate beneficial mutations

• Expel deleterious mutations

• Bacteria through HGT

•Viruses!

Recombination

Recombination and phylogeny

X

A

B

C

D

E

FG

H

I

A

B

C

D

E

FG

H

I

H

Recombination and phylogeny

X

A

B

C

D

E

FG

H

I

H

Phylogenetic networks

X

A

B

C

DE

FG

H

I

H

Methods for detection of recombinants

-Detecting conflicting phylogenetic signals

•Phylogenetic networks (SplitsTree)

•Can be due to recombination or homoplasy

Phylogenetic network

Methods for detection of recombinants

-Analyze conflicting phylogenetic signals, recombination vs homoplasy, and define breakpoints

•Bootscan (SimPlot)

•Similarity plots (SimPlot)

•Statistical tests (phi-test)

•RDP, Geneconv, MaxChi, Chimaera, SisScan, 3Sec, LARD, Topal, …. (RDP)

Bootscan