Bayesian Reconstruction of Coevolutionary Histories

Talk about my work that I gave to the Computational Evolution Group at The University of Auckland.

Transcript

1. Introduction Methods Results Closing Remarks Bayesian Reconstruction of Coevolutionary Histories Arman Bilge March 13, 2013 x Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
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3. Introduction Methods Results Closing Remarks How should we compare the phylogenies of symbionts? Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
4. Introduction Methods Results Closing Remarks How should we compare the phylogenies of symbionts? Encephalartos Encephalartos associations associations Amorphocerini Amorphocerini E._princeps Propor E._cycadifolius A._setosus E._friderici-guilielmi A._rufipes E._ghellinckii E._altensteinii A._talpa E._trispinosus E._longifolius E._arenarius E._latifrons E._lehmannii A.sp._n._1 A.sp._n._4 P._zamiae P._dissimilis E._hildebrandtii P._gedyei P._hispidus E._senticosus P.sp._n._1 P.sp._n._2 P.sp._n._3 E._horridus P.sp._n._4 P.sp._n._5 E._villosus P.sp._n._6 E._ferox P.sp._n._7 E._laevifolius P.sp._n._8 P.sp._n._9 E._caffer P.sp._n._11 E._umbeluziensis P.sp._n._12 E._aplanatus P.sp._n._13 P.sp._n._14 E._natalensis E._lebomboensis Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
5. Introduction Methods Results Closing Remarks The Cophylogeny Reconciliation Problem What were the ancestral host–symbiont partnerships? Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
6. Introduction Methods Results Closing Remarks The Cophylogeny Reconciliation Problem What were the ancestral host–symbiont partnerships? Like ancestral state reconstruction, except with prior on rate matrix based on host phylogeny Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
7. Introduction Methods Results Closing Remarks The Cophylogeny Reconciliation Problem What were the ancestral host–symbiont partnerships? Like ancestral state reconstruction, except with prior on rate matrix based on host phylogeny Discrepancies between host and symbiont phylogenies explained by coevolutionary events Cospeciation, duplication, host-switch, and loss x Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
8. Introduction Methods Results Closing Remarks The Cophylogeny Reconciliation Problem What were the ancestral host–symbiont partnerships? Like ancestral state reconstruction, except with prior on rate matrix based on host phylogeny Discrepancies between host and symbiont phylogenies explained by coevolutionary events Cospeciation, duplication, host-switch, and loss Also applies to gene tree–species tree reconciliation, particularly involving horizontal transfer events x Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
9. Introduction Methods Results Closing Remarks Existing Work on the Cophylogeny Reconciliation Problem Parsimony Methods Tarzan, CoRe-PA, Jane, TreeMap, AnGST, RANGER-DTL Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
10. Introduction Methods Results Closing Remarks Existing Work on the Cophylogeny Reconciliation Problem Parsimony Methods Tarzan, CoRe-PA, Jane, TreeMap, AnGST, RANGER-DTL Both trees must be fixed—no accommodation for uncertainty Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
11. Introduction Methods Results Closing Remarks Existing Work on the Cophylogeny Reconciliation Problem Parsimony Methods Tarzan, CoRe-PA, Jane, TreeMap, AnGST, RANGER-DTL Both trees must be fixed—no accommodation for uncertainty How to assign penalties to events or weigh numerous equally parsimonious solutions? Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
12. Introduction Methods Results Closing Remarks Existing Work on the Cophylogeny Reconciliation Problem Parsimony Methods Tarzan, CoRe-PA, Jane, TreeMap, AnGST, RANGER-DTL Both trees must be fixed—no accommodation for uncertainty How to assign penalties to events or weigh numerous equally parsimonious solutions? Primitive consideration of node timing info Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
13. Introduction Methods Results Closing Remarks Existing Work on the Cophylogeny Reconciliation Problem Parsimony Methods Tarzan, CoRe-PA, Jane, TreeMap, AnGST, RANGER-DTL Both trees must be fixed—no accommodation for uncertainty How to assign penalties to events or weigh numerous equally parsimonious solutions? Primitive consideration of node timing info No consideration of geographical data Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
14. Introduction Methods Results Closing Remarks Existing Work on the Cophylogeny Reconciliation Problem Parsimony Methods Tarzan, CoRe-PA, Jane, TreeMap, AnGST, RANGER-DTL Both trees must be fixed—no accommodation for uncertainty How to assign penalties to events or weigh numerous equally parsimonious solutions? Primitive consideration of node timing info No consideration of geographical data Probabilistic Methods Huelsenbeck et al. (2000), Charleston (2009), Faria et al. (2013), JPrIME DLTRS model Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
15. Introduction Methods Results Closing Remarks Existing Work on the Cophylogeny Reconciliation Problem Parsimony Methods Tarzan, CoRe-PA, Jane, TreeMap, AnGST, RANGER-DTL Both trees must be fixed—no accommodation for uncertainty How to assign penalties to events or weigh numerous equally parsimonious solutions? Primitive consideration of node timing info No consideration of geographical data Probabilistic Methods Huelsenbeck et al. (2000), Charleston (2009), Faria et al. (2013), JPrIME DLTRS model Each relies on various assumptions and simplifications Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
16. Introduction Methods Results Closing Remarks A Bayesian Interpretation of Cophylogeny probability of reconstruction P H, S, R | D H = host tree, S = symbiont tree, R = reconciliation, θ = model parameters, D = (dH, dS ) = sequence data Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
17. Introduction Methods Results Closing Remarks A Bayesian Interpretation of Cophylogeny probability of reconstruction P H, S, R | D ∝ θ likelihood P dH, dS | H, S, R, θ prior P (H, S, R, θ) dθ H = host tree, S = symbiont tree, R = reconciliation, θ = model parameters, D = (dH, dS ) = sequence data Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
18. Introduction Methods Results Closing Remarks A Bayesian Interpretation of Cophylogeny probability of reconstruction P H, S, R | D ∝ θ likelihood P dH, dS | H, S, R, θ prior P (H, S, R, θ) dθ Likelihood P dH, dS | H, S, R, θ = P dH | H, S, R, θ P dS | H, S, R, θ H = host tree, S = symbiont tree, R = reconciliation, θ = model parameters, D = (dH, dS ) = sequence data Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
19. Introduction Methods Results Closing Remarks A Bayesian Interpretation of Cophylogeny probability of reconstruction P H, S, R | D ∝ θ likelihood P dH, dS | H, S, R, θ prior P (H, S, R, θ) dθ Likelihood P dH, dS | H, S, R, θ = P dH | H, S, R, θ P dS | H, S, R, θ = P dH | H tree likelihood P dS | S tree likelihood H = host tree, S = symbiont tree, R = reconciliation, θ = model parameters, D = (dH, dS ) = sequence data Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
20. Introduction Methods Results Closing Remarks A Bayesian Interpretation of Cophylogeny probability of reconstruction P H, S, R | D ∝ θ likelihood P dH, dS | H, S, R, θ prior P (H, S, R, θ) dθ Prior P (H, S, R, θ) = P S | H, R, θ P (H, R, θ) H = host tree, S = symbiont tree, R = reconciliation, θ = model parameters, D = (dH, dS ) = sequence data Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
21. Introduction Methods Results Closing Remarks A Bayesian Interpretation of Cophylogeny probability of reconstruction P H, S, R | D ∝ θ likelihood P dH, dS | H, S, R, θ prior P (H, S, R, θ) dθ Prior P (H, S, R, θ) = P S | H, R, θ P (H, R, θ) = P S | H, R, θ ? P (H) P (R) P (θ) existing/trivial priors H = host tree, S = symbiont tree, R = reconciliation, θ = model parameters, D = (dH, dS ) = sequence data Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
22. Introduction Methods Results Closing Remarks Computing P S | H, R, θ There are infinite histories that may yield S under H and R Particularly confounding due to loss events Probability cannot be integrated analytically Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
23. Introduction Methods Results Closing Remarks Computing P S | H, R, θ There are infinite histories that may yield S under H and R Particularly confounding due to loss events Probability cannot be integrated analytically As a simplification, I consider only “observable” events Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
24. Introduction Methods Results Closing Remarks Computing P S | H, R, θ There are infinite histories that may yield S under H and R Particularly confounding due to loss events Probability cannot be integrated analytically As a simplification, I consider only “observable” events Assume that symbiont always cospeciates with its host Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
25. Introduction Methods Results Closing Remarks Computing P S | H, R, θ There are infinite histories that may yield S under H and R Particularly confounding due to loss events Probability cannot be integrated analytically As a simplification, I consider only “observable” events Assume that symbiont always cospeciates with its host Other events independent of host and modelled as Poisson processes with independent rates Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
26. Introduction Methods Results Closing Remarks Computing P S | H, R, θ There are infinite histories that may yield S under H and R Particularly confounding due to loss events Probability cannot be integrated analytically As a simplification, I consider only “observable” events Assume that symbiont always cospeciates with its host Other events independent of host and modelled as Poisson processes with independent rates Symbiont and host must be contemporaneous Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
27. Introduction Methods Results Closing Remarks Computing P S | H, R, θ h0 h1 h2 Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
28. Introduction Methods Results Closing Remarks Computing P S | H, R, θ h0 h1 h2 What is the relationship of h0 to h1 and h2 in the host tree? Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
29. Introduction Methods Results Closing Remarks Computing P S | H, R, θ h0 h1 h2 What is the relationship of h0 to h1 and h2 in the host tree? Either self, child/parent, or sister/cousin Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
30. Introduction Methods Results Closing Remarks Computing P S | H, R, θ h0 h1 h2 What is the relationship of h0 to h1 and h2 in the host tree? Either self, child/parent, or sister/cousin Permutation of two relationships yields potential scenarios Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
31. Introduction Methods Results Closing Remarks Computing P S | H, R, θ : The Scenarios Introduction Methods Simulation Results Closing Remarks The Cases x x x x Host / Symbiont Bayesian Reconstruction of Coevolutionary Histories Arman Bilge Host / Symbiont Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
32. Introduction Methods Results Closing Remarks Computing P S | H, R, θ : An Example Scenario x Host / Symbiont Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
33. Introduction Methods Results Closing Remarks Computing P S | H, R, θ : An Example Scenario x Host / Symbiont Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
34. Introduction Methods Results Closing Remarks Computing P S | H, R, θ : An Example Scenario x Host / Symbiont Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
35. Introduction Methods Results Closing Remarks Computing P S | H, R, θ : An Example Scenario x Host / Symbiont Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
36. Introduction Methods Results Closing Remarks Computing P S | H, R, θ : An Example Scenario x x Host / Symbiont Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
37. Introduction Methods Results Closing Remarks Computing P S | H, R, θ : An Example Scenario x Host / Symbiont Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
38. Introduction Methods Results Closing Remarks Operating on the Reconciliation Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
39. Introduction Methods Results Closing Remarks Operating on the Reconciliation Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
40. Introduction Methods Results Closing Remarks Operating on the Reconciliation Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
41. Introduction Methods Results Closing Remarks Operating on the Reconciliation x Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
42. Introduction Methods Results Closing Remarks Implementation Details θ = (λ, τ, µ), rates for duplication, host-switch, and loss Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
43. Introduction Methods Results Closing Remarks Implementation Details θ = (λ, τ, µ), rates for duplication, host-switch, and loss Introduce rate factor κ represented by clock model Fix µ = 1 Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
44. Introduction Methods Results Closing Remarks Implementation Details θ = (λ, τ, µ), rates for duplication, host-switch, and loss Introduce rate factor κ represented by clock model Fix µ = 1 Place uniform prior on κ and gamma priors on λ and τ; scale operator on all Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
45. Introduction Methods Results Closing Remarks Implementation Details θ = (λ, τ, µ), rates for duplication, host-switch, and loss Introduce rate factor κ represented by clock model Fix µ = 1 Place uniform prior on κ and gamma priors on λ and τ; scale operator on all Uniform prior on R, but restricted by leaf–leaf mapping Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
46. Introduction Methods Results Closing Remarks Implementation Details θ = (λ, τ, µ), rates for duplication, host-switch, and loss Introduce rate factor κ represented by clock model Fix µ = 1 Place uniform prior on κ and gamma priors on λ and τ; scale operator on all Uniform prior on R, but restricted by leaf–leaf mapping Implemented as plugin for BEAST1 Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
47. Introduction Methods Results Closing Remarks Simulation Methodology Simple simulation pipeline 1. Host tree generated under constant size coalescent 2. DNA simulated on host tree under JC69 model 3. Symbiont tree generated on host tree under described model (three Poisson processes) 4. DNA simulated on symbiont tree under JC69 for all extant taxa Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
48. Introduction Methods Results Closing Remarks Simulation Methodology Simple simulation pipeline 1. Host tree generated under constant size coalescent 2. DNA simulated on host tree under JC69 model 3. Symbiont tree generated on host tree under described model (three Poisson processes) 4. DNA simulated on symbiont tree under JC69 for all extant taxa 1st simulation: 8 host taxa, all event rates 0 (identical trees) Accurate reconstruction with posterior P ≥ 0.99 Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
49. Introduction Methods Results Closing Remarks Simulation Methodology Simple simulation pipeline 1. Host tree generated under constant size coalescent 2. DNA simulated on host tree under JC69 model 3. Symbiont tree generated on host tree under described model (three Poisson processes) 4. DNA simulated on symbiont tree under JC69 for all extant taxa 1st simulation: 8 host taxa, all event rates 0 (identical trees) Accurate reconstruction with posterior P ≥ 0.99 2nd simulation: 8 host taxa, all event rates 1.0, 8 symbionts Trees reconstructed accurately, reconciliation questionable... Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
50. Introduction Methods Results Closing Remarks Results from Second Simulation median 95% HPD λ 1.42 [0.10, 4.63] τ 2.48 [0.20, 9.18] µ 1.60 [0.11, 7.24] 0.079 0.053 0.365 symbiont5.1 0.615 0.079 0.984 0.053 0.365 0.366 symbiont3.3 symbiont7.1 symbiont8.1 symbiont5.1 symbiont5.2 symbiont3.1 0.607 symbiont8.2 Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
51. Introduction Methods Results Closing Remarks Contributions Formulated an expression for the posterior probability of a cophylogenetic reconstruction Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
52. Introduction Methods Results Closing Remarks Contributions Formulated an expression for the posterior probability of a cophylogenetic reconstruction Developed an algorithm to approximate the probability of a symbiont tree for a reconstruction Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
53. Introduction Methods Results Closing Remarks Contributions Formulated an expression for the posterior probability of a cophylogenetic reconstruction Developed an algorithm to approximate the probability of a symbiont tree for a reconstruction Implemented the algorithm in an MCMC framework Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
54. Introduction Methods Results Closing Remarks Open Questions and Problems Detecting Cospeciation Technically only occurs when host and symbiont speciate at the same time Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
55. Introduction Methods Results Closing Remarks Open Questions and Problems Detecting Cospeciation Technically only occurs when host and symbiont speciate at the same time Important for identifying between some scenarios x x x Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
56. Introduction Methods Results Closing Remarks Open Questions and Problems Is this an appropriate approximation technique? Rigorous definition for an observable event? Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
57. Introduction Methods Results Closing Remarks Open Questions and Problems Is this an appropriate approximation technique? Rigorous definition for an observable event? Can we place an informative prior on the reconciliation? P (H, R, θ) = P R | H, θ P (H) P (θ) We have a node–node mapping R, but do not know nodal relationships for one tree Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
58. Introduction Methods Results Closing Remarks Open Questions and Problems Is this an appropriate approximation technique? Rigorous definition for an observable event? Can we place an informative prior on the reconciliation? P (H, R, θ) = P R | H, θ P (H) P (θ) We have a node–node mapping R, but do not know nodal relationships for one tree What is the effect of the operator on mixing? Cophylogeny model substantially fragments posterior landscape—a wrong move makes the reconciliation invalid Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
59. Introduction Methods Results Closing Remarks Open Questions and Problems Is this an appropriate approximation technique? Rigorous definition for an observable event? Can we place an informative prior on the reconciliation? P (H, R, θ) = P R | H, θ P (H) P (θ) We have a node–node mapping R, but do not know nodal relationships for one tree What is the effect of the operator on mixing? Cophylogeny model substantially fragments posterior landscape—a wrong move makes the reconciliation invalid How best can we evaluate the model performance via simulation studies? Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
60. Introduction Methods Results Closing Remarks Open Questions and Problems Are the event rates better predicted by the symbiont or host? Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
61. Introduction Methods Results Closing Remarks Open Questions and Problems Are the event rates better predicted by the symbiont or host? Model for host speciating independently of symbiont (a.k.a. failure to diverge event)? Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
62. Introduction Methods Results Closing Remarks Open Questions and Problems Are the event rates better predicted by the symbiont or host? Model for host speciating independently of symbiont (a.k.a. failure to diverge event)? Can we consider preferential host-switching in the model? Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
63. Introduction Methods Results Closing Remarks Open Questions and Problems Are the event rates better predicted by the symbiont or host? Model for host speciating independently of symbiont (a.k.a. failure to diverge event)? Can we consider preferential host-switching in the model? Can we consider geography in the model? An associated host and symbiont must be cohabiting Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
64. Introduction Methods Results Closing Remarks Open Questions and Problems Are the event rates better predicted by the symbiont or host? Model for host speciating independently of symbiont (a.k.a. failure to diverge event)? Can we consider preferential host-switching in the model? Can we consider geography in the model? An associated host and symbiont must be cohabiting How can we visualise the reconstruction? Reconciling the trees does not recover the events Several uncertainties in event timing, etc. Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
65. Introduction Methods Results Closing Remarks Open Questions and Problems Are the event rates better predicted by the symbiont or host? Model for host speciating independently of symbiont (a.k.a. failure to diverge event)? Can we consider preferential host-switching in the model? Can we consider geography in the model? An associated host and symbiont must be cohabiting How can we visualise the reconstruction? Reconciling the trees does not recover the events Several uncertainties in event timing, etc. Can we test coevolutionary theories, e.g. GMTC or escape-and-radiate? Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
66. Introduction Methods Results Closing Remarks Acknowledgements My mentors, Dr. Yi-Chieh Jessica Wu, Rachel Sealfon, and Prof. Mukul Bansal Andrew Brownjohn, Jon Sanders, Prof. Ran Libeskind-Hadas, Hayden Metsky, and Prof. Manolis Kellis, for helpful discussions Dr. Susan Offner, for inspiring me Bayesian Reconstruction of Coevolutionary Histories Arman Bilge