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Bayesian Reconstruction of Coevolutionary Histories

Bayesian Reconstruction of Coevolutionary Histories

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

Arman Bilge

March 13, 2014
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  1. Introduction Methods Results Closing Remarks Bayesian Reconstruction of Coevolutionary Histories

    Arman Bilge March 13, 2013 x Bayesian Reconstruction of Coevolutionary Histories Arman Bilge
  2. Introduction Methods Results Closing Remarks Phylogenetic Evidence for Cycad–Weevil Coevolution

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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