Introduction                      Early Warning         Conclusions                        Acknowledgements       Regime s...
Introduction                      Early Warning         Conclusions                        Acknowledgements Carl Boettiger...
Introduction                      Early Warning         Conclusions                        Acknowledgements Carl Boettiger...
Introduction                      Early Warning         Conclusions                        AcknowledgementsRegime Carl Boe...
Introduction                      Early Warning         Conclusions                        AcknowledgementsShifts Carl Boe...
Introduction                      Early Warning              Conclusions                        Acknowledgements          ...
Introduction                      Early Warning         Conclusions                        Acknowledgementsstarted in phys...
Introduction                      Early Warning         Conclusions                        AcknowledgementsDigging for din...
Introduction                      Early Warning         Conclusions                        Acknowledgements               ...
Introduction                      Early Warning          Conclusions                       AcknowledgementsPeter’s dives C...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements               ...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       AcknowledgementsHow do we get a...
Introduction                       Early Warning                    Conclusions                          Acknowledgements ...
Introduction                      Early Warning          Conclusions                       Acknowledgements       Candidat...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                       Early Warning                        Conclusions                       Acknowledgements...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning             Conclusions                       Acknowledgements            ...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       AcknowledgementsCoral Bleaching...
Introduction                      Early Warning          Conclusions                       AcknowledgementsEutrophication ...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements               ...
Introduction                      Early Warning          Conclusions                       AcknowledgementsCarver Carl Boe...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       Acknowledgements Carl Boettiger...
Introduction                      Early Warning          Conclusions                       AcknowledgementsUnifying challe...
Introduction                      Early Warning          Conclusions                       AcknowledgementsUnifying challe...
Introduction                      Early Warning          Conclusions                       AcknowledgementsUnifying challe...
Introduction                      Early Warning          Conclusions                       AcknowledgementsUnifying challe...
Introduction                      Early Warning          Conclusions                       AcknowledgementsWhy Open Source...
Introduction                      Early Warning          Conclusions                       Acknowledgements   Code   Liter...
Introduction                      Early Warning          Conclusions                       AcknowledgementsThe Open Lab No...
Introduction                      Early Warning          Conclusions                              AcknowledgementsAcknowle...
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Regime shifts in ecology and evolution

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Regime shifts in ecology and evolution

  1. 1. Introduction Early Warning Conclusions Acknowledgements Regime shifts in ecology & evolution @cboettig Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 1/45
  2. 2. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 2/45
  3. 3. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 3/45
  4. 4. Introduction Early Warning Conclusions AcknowledgementsRegime Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 4/45
  5. 5. Introduction Early Warning Conclusions AcknowledgementsShifts Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 5/45
  6. 6. Introduction Early Warning Conclusions Acknowledgements Ecologist Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 6/45
  7. 7. Introduction Early Warning Conclusions Acknowledgementsstarted in physics. . . Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 7/45
  8. 8. Introduction Early Warning Conclusions AcknowledgementsDigging for dinosaurs sponsored by National Geographic Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 8/45
  9. 9. Introduction Early Warning Conclusions Acknowledgements Peter Wainwright Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 9/45
  10. 10. Introduction Early Warning Conclusions AcknowledgementsPeter’s dives Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 10/45
  11. 11. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 11/45
  12. 12. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 12/45
  13. 13. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 13/45
  14. 14. Introduction Early Warning Conclusions Acknowledgements A release of constraint? Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 14/45
  15. 15. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 15/45
  16. 16. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 16/45
  17. 17. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 17/45
  18. 18. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 18/45
  19. 19. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 19/45
  20. 20. Introduction Early Warning Conclusions AcknowledgementsHow do we get anevolutionary time seriesfrom present-day species? Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 20/45
  21. 21. Introduction Early Warning Conclusions Acknowledgements XT1 = X0 e−α1 T1 + n where you start γi = − αj tj −α1 T1 j=i+1 θ1 1 − e + Where you are going T1 σ1 eα1 (s−T1 ) dWs 0 Random shocks along the waySolves as: n E(Xi ) = eγi θi 1 − eαi ti i=0 k 2 σs Cov(Xi , Xj ) = eγs +γs 1 − e−2αs ts s=0 2αs Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 21/45
  22. 22. Introduction Early Warning Conclusions Acknowledgements Candidate models Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 22/45
  23. 23. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 23/45
  24. 24. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 24/45
  25. 25. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 25/45
  26. 26. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 26/45
  27. 27. Introduction Early Warning Conclusions Acknowledgements Phylogenetic Monte Carlo x p le om comdel → e fr → mo ulat odel Sim ple m sim l s mode ts both ← Fi is data to th LogLik(complex) LogLik(simple) frequency Likelihood ratio Boettiger et al. 2012, Evolution, pmc R package Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 27/45
  28. 28. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 28/45
  29. 29. Introduction Early Warning Conclusions Acknowledgements Part II Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 29/45
  30. 30. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 30/45
  31. 31. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 31/45
  32. 32. Introduction Early Warning Conclusions AcknowledgementsCoral Bleaching Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 32/45
  33. 33. Introduction Early Warning Conclusions AcknowledgementsEutrophication Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 33/45
  34. 34. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 34/45
  35. 35. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 35/45
  36. 36. Introduction Early Warning Conclusions Acknowledgements d E(xi ) = 2 r(t)( r(t) + θ − xi ) (1) dt d V (xi ) = −2 r(t)V (xi ) + σ 2 ( r(t) + θ) (2) dt Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 36/45
  37. 37. Introduction Early Warning Conclusions AcknowledgementsCarver Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 37/45
  38. 38. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC al. 2012, PRSI Boettiger et Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 38/45
  39. 39. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 39/45
  40. 40. Introduction Early Warning Conclusions Acknowledgements Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 40/45
  41. 41. Introduction Early Warning Conclusions AcknowledgementsUnifying challenges in regime shifts Weak signals Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 41/45
  42. 42. Introduction Early Warning Conclusions AcknowledgementsUnifying challenges in regime shifts Weak signals Uncertainty quantification Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 41/45
  43. 43. Introduction Early Warning Conclusions AcknowledgementsUnifying challenges in regime shifts Weak signals Uncertainty quantification Computationally intensive Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 41/45
  44. 44. Introduction Early Warning Conclusions AcknowledgementsUnifying challenges in regime shifts Weak signals Uncertainty quantification Computationally intensive Statistical power is data limited Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 41/45
  45. 45. Introduction Early Warning Conclusions AcknowledgementsWhy Open Source? Reproduce research Find & fix bugs Extend into new software Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 42/45
  46. 46. Introduction Early Warning Conclusions Acknowledgements Code Literature Discussions Lab Notebook Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 43/45
  47. 47. Introduction Early Warning Conclusions AcknowledgementsThe Open Lab Notebook Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 44/45
  48. 48. Introduction Early Warning Conclusions AcknowledgementsAcknowledgements Image credits Michael Najjar Arkive.org Millennium Ecosystem Assessment Flickr user gfpeck Boettiger et al 2012 Scheffer et al. 2001 Westneat & Alfaro 2005 http://carlboettiger.info/ Carl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 45/45

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