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Viral Evolution and Recombination

Viral Evolution and Recombination. Peter Norberg peter.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…

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Viral Evolution and Recombination

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  1. Viral Evolution and Recombination • Peter Norberg • peter.norberg@gu.se

  2. Phylogenetic analysis • Reconstruction of evolutionary history • Relationship • Distance • Common ancestors

  3. Tree of Life

  4. Viruses and Viral Evolution • Viruses are not living organisms! • but evolving… • Genetic material (DNA or RNA) • Need to adapt to their environment!

  5. A B C D A C B D A A A B B B C C C D D D Different representations of phylogenetic trees

  6. 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

  7. Bootstrapping A: AACTTAACCACGCTATCGATGCAATTATATA B: AATTTGACTGCGGTACCGATCCAATTATATA C: AATTTGACTGGGCTACCGATCCAATTATATA D: AACTTAACCGCGCTACTGATCGAATTATATA A: CACC B: TGCT C: TGCT D: CAGC A C B D A B C D A D B C 1 3 96 1 3 96

  8. 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!

  9. Recombination

  10. C C A A D D E E H H B B I I F F G G Recombination and phylogeny X H

  11. Recombination and phylogeny X H C A D E H B I F G

  12. Phylogenetic networks X H C A D E H B I F G

  13. Methods for detection of recombinants • -Detecting conflicting phylogenetic signals • Phylogenetic networks (SplitsTree) • Can be due to recombination or homoplasy

  14. Phylogenetic network

  15. 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)

  16. Bootscan

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