A new non-minimal algorithm for dating phylogenies of fossil taxa   Graeme T. Lloyd, Matt Friedman and               Mark ...
Molecular phylogeny                      (dos Reis et al. 2012)
Palaeontological phylogeny                             (Motani 1999)
But what about extinct clades?
Branch lengths in palaeontology
“Ghost” diversity                     Raw                              Raw + “ghosts”       Raw + “ghosts”                ...
Extinction survival                      Aphylogenetic survival:                      1/3 = 33%                      Phylo...
Evolutionary rates                     (Lloyd et al. 2012)
Phylogenetic covariance matrix                    A    B    D      E    F     G                  A 15 1      0     0     0...
Evolutionary modelsBrownian Motion      Early Burst          TrendOrnstein-Uhlenbeck   Late Burst                         ...
A brief history of fossil-only         tree dating
Traditional approachτ8τ7                 = max(   ,   ) = max(τ8,τ7)τ6τ5τ4τ3τ2τ1                                          ...
Traditional approachτ8τ7                 Implied phylogenyτ6τ5τ4τ3τ2τ1                                       (Smith 1994)
Add k solutionτ8τ7                    = max(   ,   )+kτ6τ5τ4τ3τ2          kτ1                                    (Derstler...
Branch sharing solution                                       Share time with preceding     Traditional approach first    ...
A novel approach
Hedman approachτ8                       = ƒ(            )τ7τ6τ5τ4τ3τ2τ1                              (Hedman 2010)
Hedman approachFrequency                                         t0                        Age (Ma)            Minimum    ...
Hedman approachτ8                       = ƒ(            )τ7τ6                     = ƒ(            )τ5τ4τ3τ2τ1             ...
Hedman approach                  Only 135 ‘unique’ nodes                  (one third of 416 total)                        ...
Hedman approach                  Only 135 ‘unique’ nodes                  (one third of 416 total)                  What a...
Modified Hedman approach
Modified Hedman approach
Modified Hedman approach            1                2                    3
Modified Hedman approach                    1                        2                            3Min           Max
Modified Hedman approach                        1                            2                                3      1   2...
Modified Hedman approach            1                2                    3
Molecular versus fossil-only dating in        placental mammals
Placental mammals               • Informal supertree               • 48 source trees               • 452 OTUs (cladistical...
Fossil vs. Molecular dates                               Cretaceous                   Paleogene      Cretaceous      Paleo...
Traditional vs. Molecular                                                        Cretaceous                               ...
New approach vs. Molecular                                                            Cretaceous                          ...
Approach comparison                 Meredith  Traditional                  et al.   approach                  2011  Modifi...
Approach comparison                          Meredith  Traditional   1:1 RSS                           et al.   approach  ...
Approach comparison                          Meredith  Traditional                           et al.   approach            ...
Conclusions• Novel fossil-only tree dating approach
Conclusions• Novel fossil-only tree dating approach• Mimics molecular approach (distribution)
Conclusions• Novel fossil-only tree dating approach• Mimics molecular approach (distribution)• Helps close molecule-fossil...
Conclusions•    Novel fossil-only tree dating approach•    Mimics molecular approach (distribution)•    Helps close molecu...
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A new non-minimal algorithm for dating phylogenies of fossil taxa

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A new non-minimal algorithm for dating phylogenies of fossil taxa

  1. 1. A new non-minimal algorithm for dating phylogenies of fossil taxa Graeme T. Lloyd, Matt Friedman and Mark A. Bell
  2. 2. Molecular phylogeny (dos Reis et al. 2012)
  3. 3. Palaeontological phylogeny (Motani 1999)
  4. 4. But what about extinct clades?
  5. 5. Branch lengths in palaeontology
  6. 6. “Ghost” diversity Raw Raw + “ghosts” Raw + “ghosts” Raw (Weishampel et Jianu 2000) (Brusatte et al. 2011)
  7. 7. Extinction survival Aphylogenetic survival: 1/3 = 33% Phylogenetic survival: 4/6 = 67% (Modesto et al. 2001)
  8. 8. Evolutionary rates (Lloyd et al. 2012)
  9. 9. Phylogenetic covariance matrix A B D E F G A 15 1 0 0 0 0 B 1 15 0 0 0 0 D 0 0 15 14 7 7 E 0 0 14 15 7 7 F 0 0 7 7 15 9 G 0 0 7 7 9 15 (Slide pilfered from Chris Organ)
  10. 10. Evolutionary modelsBrownian Motion Early Burst TrendOrnstein-Uhlenbeck Late Burst (Slides pilfered from Graham Slater)
  11. 11. A brief history of fossil-only tree dating
  12. 12. Traditional approachτ8τ7 = max( , ) = max(τ8,τ7)τ6τ5τ4τ3τ2τ1 (Smith 1994)
  13. 13. Traditional approachτ8τ7 Implied phylogenyτ6τ5τ4τ3τ2τ1 (Smith 1994)
  14. 14. Add k solutionτ8τ7 = max( , )+kτ6τ5τ4τ3τ2 kτ1 (Derstler 1982; Forey 1988)
  15. 15. Branch sharing solution Share time with preceding Traditional approach first (non-zero length) branchτ8τ7 τ7τ6 τ6 root ageτ5 τ5 (Ruta et al. 2006; Brusatte et al. 2008)
  16. 16. A novel approach
  17. 17. Hedman approachτ8 = ƒ( )τ7τ6τ5τ4τ3τ2τ1 (Hedman 2010)
  18. 18. Hedman approachFrequency t0 Age (Ma) Minimum Maximum
  19. 19. Hedman approachτ8 = ƒ( )τ7τ6 = ƒ( )τ5τ4τ3τ2τ1 (Hedman 2010)
  20. 20. Hedman approach Only 135 ‘unique’ nodes (one third of 416 total) (Lloyd et al. 2008)
  21. 21. Hedman approach Only 135 ‘unique’ nodes (one third of 416 total) What about the other two thirds? (Lloyd et al. 2008)
  22. 22. Modified Hedman approach
  23. 23. Modified Hedman approach
  24. 24. Modified Hedman approach 1 2 3
  25. 25. Modified Hedman approach 1 2 3Min Max
  26. 26. Modified Hedman approach 1 2 3 1 2 3Min Max
  27. 27. Modified Hedman approach 1 2 3
  28. 28. Molecular versus fossil-only dating in placental mammals
  29. 29. Placental mammals • Informal supertree • 48 source trees • 452 OTUs (cladistically placed) • Computation time: 6m 57s
  30. 30. Fossil vs. Molecular dates Cretaceous Paleogene Cretaceous Paleogene
  31. 31. Traditional vs. Molecular Cretaceous Paleogene 1:1 RSS 31269.3 Traditional approach Cretaceous Paleogene Meredith et al. 2011
  32. 32. New approach vs. Molecular Cretaceous Paleogene Modified Hedman approach 1:1 RSS 1:1 RSS 31269.3 12340.4 Cretaceous Paleogene Meredith et al. 2011
  33. 33. Approach comparison Meredith Traditional et al. approach 2011 Modified dos Reis Hedman et al. approach 2012
  34. 34. Approach comparison Meredith Traditional 1:1 RSS et al. approach 10433.7 2011 1:1 RSS 2210.1 Modified dos Reis Hedman et al. approach 2012
  35. 35. Approach comparison Meredith Traditional et al. approach 2011 1:1 RSS 1837.6 Modified dos Reis 1:1 RSS Hedman et al. 1514.9 approach 2012
  36. 36. Conclusions• Novel fossil-only tree dating approach
  37. 37. Conclusions• Novel fossil-only tree dating approach• Mimics molecular approach (distribution)
  38. 38. Conclusions• Novel fossil-only tree dating approach• Mimics molecular approach (distribution)• Helps close molecule-fossil gap
  39. 39. Conclusions• Novel fossil-only tree dating approach• Mimics molecular approach (distribution)• Helps close molecule-fossil gap• Implications for a wide range of topics, e.g.: • Phylogenetic diversity estimates • Extinction/Survival %s • Rates of evolution • Trait models • Better calibration distributions

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