This document describes a new algorithm for dating phylogenies using only fossil taxa. The traditional approach dates each fossil individually, but the new approach dates nodes based on a probability distribution of ages between the minimum and maximum possible ages. This mimics molecular dating approaches and helps close the gap between molecular and fossil-based timetrees. The new approach provides a significantly better fit to independently estimated molecular divergence times than the traditional approach.

1. A new non-minimal algorithm for
dating phylogenies of fossil taxa
Graeme T. Lloyd, Matt Friedman and
Mark A. Bell

2. Molecular phylogeny
(dos Reis et al. 2012)

3. Palaeontological phylogeny
(Motani 1999)

4. But what about extinct clades?

5. Branch lengths in palaeontology

6. “Ghost” diversity
Raw
Raw + “ghosts”
Raw + “ghosts”
Raw
(Weishampel et Jianu 2000) (Brusatte et al. 2011)

7. Extinction survival
Aphylogenetic survival:
1/3 = 33%
Phylogenetic survival:
4/6 = 67%
(Modesto et al. 2001)

8. Evolutionary rates
(Lloyd et al. 2012)

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. Evolutionary models
Brownian Motion Early Burst Trend
Ornstein-Uhlenbeck Late Burst
(Slides pilfered from Graham Slater)

11. A brief history of fossil-only
tree dating

12. Traditional approach
τ8
τ7 = max( , ) = max(τ8,τ7)
τ6
τ5
τ4
τ3
τ2
τ1
(Smith 1994)

13. Traditional approach
τ8
τ7 Implied phylogeny
τ6
τ5
τ4
τ3
τ2
τ1
(Smith 1994)

14. Add k solution
τ8
τ7 = max( , )+k
τ6
τ5
τ4
τ3
τ2
k
τ1
(Derstler 1982; Forey 1988)

15. Branch sharing solution
Share time with preceding
Traditional approach first
(non-zero length) branch
τ8
τ7 τ7
τ6 τ6
root age
τ5 τ5
(Ruta et al. 2006; Brusatte et al. 2008)

16. A novel approach

17. Hedman approach
τ8
= ƒ( )
τ7
τ6
τ5
τ4
τ3
τ2
τ1
(Hedman 2010)

18. Hedman approach
Frequency
t0
Age (Ma)
Minimum Maximum

19. Hedman approach
τ8
= ƒ( )
τ7
τ6 = ƒ( )
τ5
τ4
τ3
τ2
τ1
(Hedman 2010)

20. Hedman approach
Only 135 ‘unique’ nodes
(one third of 416 total)
(Lloyd et al. 2008)

21. Hedman approach
Only 135 ‘unique’ nodes
(one third of 416 total)
What about the
other two thirds?
(Lloyd et al. 2008)

22. Modified Hedman approach

23. Modified Hedman approach

24. Modified Hedman approach
1
2
3

25. Modified Hedman approach
1
2
3
Min Max

26. Modified Hedman approach
1
2
3
1 2 3
Min Max

27. Modified Hedman approach
1
2
3

28. Molecular versus fossil-only dating in
placental mammals

29. Placental mammals
• Informal supertree
• 48 source trees
• 452 OTUs (cladistically
placed)
• Computation time: 6m 57s

30. Fossil vs. Molecular dates
Cretaceous
Paleogene
Cretaceous
Paleogene

31. Traditional vs. Molecular
Cretaceous
Paleogene
1:1 RSS
31269.3
Traditional approach
Cretaceous
Paleogene
Meredith et al. 2011

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. Approach comparison
Meredith
Traditional
et al.
approach
2011
Modified dos Reis
Hedman et al.
approach 2012

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. 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. Conclusions
• Novel fossil-only tree dating approach

37. Conclusions
• Novel fossil-only tree dating approach
• Mimics molecular approach (distribution)

38. Conclusions
• Novel fossil-only tree dating approach
• Mimics molecular approach (distribution)
• Helps close molecule-fossil gap

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