1. JunglesM. A. Charleston Jungles A new solution to the host/parasite phylogeny reconciliation problem M. A. Charleston University of Glasgow m.a.charleston@bio.gla.ac.uk

2. JunglesM. A. Charleston Problem Definition Given: Host phylogeny H; Associate phylogeny P; Known associations between them . What were the past associations of taxa?

3. JunglesM. A. Charleston Host/Parasite Phylogeny Reconciliation Associations Host phylogenyAssociate Phylogeny

4. JunglesM. A. Charleston Multiple Solutions

5. JunglesM. A. Charleston The Model Parasites are independent new species after speciation. There are four event types: cospeciation, duplication, lineage sorting, and host switching.

6. JunglesM. A. Charleston The Four Event Types JunglesM. A. Charleston

7. JunglesM. A. Charleston Event Costs EventCost Cospeciation Duplication Lineage Sorting Host Switch c ≤ 0 d > 0 s > 0 w > 0

8. JunglesM. A. Charleston Jungles The Jungle is a digraph (directed graph). The vertices of the jungle are the extant & hypothesized host/parasite associations. The arcs of the jungle correspond to arcs of the associate tree. The inferred events are dependent only on the arcs in the jungle.

9. JunglesM. A. Charleston The Two J- Vertex Types

10. JunglesM. A. Charleston Jungle Arc Types - 1

11. JunglesM. A. Charleston Jungle Arc Types - 2

12. JunglesM. A. Charleston Jungle Arc Types - 3

13. JunglesM. A. Charleston JunglesM. A. Charleston Host Switching Host switching induces a partial ordering on the host tree w’ precedes x

14. JunglesM. A. Charleston Switch Incompatibility - 1 Weak Incompatibility: Temporal incongruence can be fixed by moving landing sites back in time. s 1  u’ precedes v s 2  w’ precedes x

15. JunglesM. A. Charleston Switch Incompatibility - 2 The order in which we consider host switches affects the number of induced sorting events.

16. JunglesM. A. Charleston Switch Incompatibility - 3 Strong Incompatibility: Moving the landing sites back cannot solve the temporal incongruity. s 1  u’ precedes w s 2  v’ precedes x - Impossible!

17. JunglesM. A. Charleston From Tanglegram...

18. JunglesM. A. Charleston... to Jungle

19. JunglesM. A. Charleston Jungle Traversal

20. JunglesM. A. Charleston Optimal Solutions Embedded

21. JunglesM. A. Charleston All Solutions Embedded

22. JunglesM. A. Charleston Gophers and Lice: Tanglegram

23. JunglesM. A. Charleston Gophers and Lice: Jungle

24. JunglesM. A. Charleston Page’s Solution Cospeciation Duplication Lineage Sorting Host Switch 61226122

25. JunglesM. A. Charleston Ronquist’s Solution Cospeciation Duplication Lineage Sorting Host Switch 52225222

26. JunglesM. A. Charleston Conclusions Complete representation of solution space in one figure Fast solution through dynamic programming Guarantees global optimality Correct accounting for host switches General model, extendable to maximum likelihood