Transcript Evolution of HSV-1 and VZV.

Viral Evolution and
Recombination
Peter Norberg
[email protected]
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
A
B
A
B
C
D
A
B
C
D
C
D
A
B
C
D
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
Bootstrapping
A: AACTTAACCACGCTATCGATGCAATTATATA
B: AATTTGACTGCGGTACCGATCCAATTATATA
C: AATTTGACTGGGCTACCGATCCAATTATATA
D: AACTTAACCGCGCTACTGATCGAATTATATA
A: CACC
B: TGCT
C: TGCT
D: CAGC
A
A
1
96
A
3
D
C
B
B
B
C
1
96
C
3
D
D
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
H
C
A
C
A
D
D
E
E
H
B
I
F
G
H
B
I
F
G
Recombination and phylogeny
H
X
C
A
D
E
H
B
I
F
G
Phylogenetic networks
H
X
C
A
D
E
H
B
I
F
G
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