Confidence intervals on node ageestimates in vertebrate phylogeny  Graeme T. Lloyd, Matt Friedman and              Mark A....
Molecular dating methods                           (Reis et al. 2012)
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 distance matrices            7    A                                 A   B   C            8        BTime (Ma) ...
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
Conclusions• Novel fossil-only tree dating approach• Mimics molecular approach• Helps close molecule-fossil gap
Conclusions•    Novel fossil-only tree dating approach•    Mimics molecular approach•    Helps close molecule-fossil gap• ...
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Confidence intervals on node age estimates in vertebrate phylogeny

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Confidence intervals on node age estimates in vertebrate phylogeny

  1. 1. Confidence intervals on node ageestimates in vertebrate phylogeny Graeme T. Lloyd, Matt Friedman and Mark A. Bell
  2. 2. Molecular dating methods (Reis et al. 2012)
  3. 3. But what about extinct clades?
  4. 4. Branch lengths in palaeontology
  5. 5. “Ghost” diversity Raw Raw + “ghosts” Raw + “ghosts” Raw (Weishampel et Jianu 2000) (Brusatte et al. 2011)
  6. 6. Extinction survival Aphylogenetic survival: 1/3 = 33% Phylogenetic survival: 4/6 = 67% (Modesto et al. 2001)
  7. 7. Evolutionary rates (Lloyd et al. 2012)
  8. 8. Phylogenetic distance matrices 7 A A B C 8 BTime (Ma) C A 0 3 5 B 3 0 4 9 C 5 4 0 10
  9. 9. A brief history of fossil-only tree dating
  10. 10. Traditional approachτ8τ7 = max( , ) = max(τ8,τ7)τ6τ5τ4τ3τ2τ1 (Smith 1994)
  11. 11. Traditional approachτ8τ7 Implied phylogenyτ6τ5τ4τ3τ2τ1 (Smith 1994)
  12. 12. Add k solutionτ8τ7 = max( , )+kτ6τ5τ4τ3τ2 kτ1 (Derstler 1982; Forey 1988)
  13. 13. Branch sharing solution Share time with preceding Traditional approach first (non-zero length) branchτ8τ7 τ7τ6 τ6 root ageτ5 τ5 (Ruta et al. 2006)
  14. 14. A novel approach
  15. 15. Hedman approachτ8 = ƒ( )τ7τ6τ5τ4τ3τ2τ1 (Hedman 2010)
  16. 16. Hedman approachFrequency t0 Age (Ma) Minimum Maximum
  17. 17. Hedman approachτ8 = ƒ( )τ7τ6 = ƒ( )τ5τ4τ3τ2τ1 (Hedman 2010)
  18. 18. Hedman approach Only 135 ‘unique’ nodes (one third of 416 total) (Lloyd et al. 2008)
  19. 19. Hedman approach Only 135 ‘unique’ nodes (one third of 416 total) What about the other two thirds? (Lloyd et al. 2008)
  20. 20. Modified Hedman approach
  21. 21. Modified Hedman approach
  22. 22. Modified Hedman approach 1 2 3
  23. 23. Modified Hedman approach 1 2 3Min Max
  24. 24. Modified Hedman approach 1 2 3 1 2 3Min Max
  25. 25. Modified Hedman approach 1 2 3
  26. 26. Molecular versus fossil-only dating in placental mammals
  27. 27. Placental mammals • Informal supertree • 48 source trees • 452 OTUs (cladistically placed) • Computation time: 6m 57s
  28. 28. Fossil vs. Molecular dates Cretaceous Paleogene Cretaceous Paleogene
  29. 29. Traditional vs. Molecular Cretaceous Paleogene 1:1 RSS 31269.3 Traditional approach Cretaceous Paleogene Meredith et al. 2011
  30. 30. 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
  31. 31. Approach comparison Meredith Traditional et al. approach 2011 Modified Reis Hedman et al. approach 2012
  32. 32. Approach comparison Meredith Traditional 1:1 RSS et al. approach 10433.7 2011 1:1 RSS 2210.1 Modified Reis Hedman et al. approach 2012
  33. 33. Approach comparison Meredith Traditional et al. approach 2011 1:1 RSS 1837.6 Modified Reis 1:1 RSS Hedman et al. 1514.9 approach 2012
  34. 34. Conclusions• Novel fossil-only tree dating approach
  35. 35. Conclusions• Novel fossil-only tree dating approach• Mimics molecular approach
  36. 36. Conclusions• Novel fossil-only tree dating approach• Mimics molecular approach• Helps close molecule-fossil gap
  37. 37. Conclusions• Novel fossil-only tree dating approach• Mimics molecular approach• 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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