Confidence intervals on node age estimates in vertebrate phylogeny
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Confidence intervals on node age estimates in vertebrate phylogeny
- 1. Confidence intervals on node age estimates in vertebrate phylogeny Graeme T. Lloyd, Matt Friedman and Mark A. Bell
- 2. Molecular dating methods (Reis et al. 2012)
- 3. But what about extinct clades?
- 4. Branch lengths in palaeontology
- 5. “Ghost” diversity Raw Raw + “ghosts” Raw + “ghosts” Raw (Weishampel et Jianu 2000) (Brusatte et al. 2011)
- 6. Extinction survival Aphylogenetic survival: 1/3 = 33% Phylogenetic survival: 4/6 = 67% (Modesto et al. 2001)
- 7. Evolutionary rates (Lloyd et al. 2012)
- 8. Phylogenetic distance matrices 7 A A B C 8 B Time (Ma) C A 0 3 5 B 3 0 4 9 C 5 4 0 10
- 9. A brief history of fossil-only tree dating
- 10. Traditional approach τ8 τ7 = max( , ) = max(τ8,τ7) τ6 τ5 τ4 τ3 τ2 τ1 (Smith 1994)
- 11. Traditional approach τ8 τ7 Implied phylogeny τ6 τ5 τ4 τ3 τ2 τ1 (Smith 1994)
- 12. Add k solution τ8 τ7 = max( , )+k τ6 τ5 τ4 τ3 τ2 k τ1 (Derstler 1982; Forey 1988)
- 13. 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)
- 14. A novel approach
- 15. Hedman approach τ8 = ƒ( ) τ7 τ6 τ5 τ4 τ3 τ2 τ1 (Hedman 2010)
- 16. Hedman approach Frequency t0 Age (Ma) Minimum Maximum
- 17. Hedman approach τ8 = ƒ( ) τ7 τ6 = ƒ( ) τ5 τ4 τ3 τ2 τ1 (Hedman 2010)
- 18. Hedman approach Only 135 ‘unique’ nodes (one third of 416 total) (Lloyd et al. 2008)
- 19. 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 1 2 3
- 23. Modified Hedman approach 1 2 3 Min Max
- 24. Modified Hedman approach 1 2 3 1 2 3 Min Max
- 25. Modified Hedman approach 1 2 3
- 26. Molecular versus fossil-only dating in placental mammals
- 27. Placental mammals • Informal supertree • 48 source trees • 452 OTUs (cladistically placed) • Computation time: 6m 57s
- 28. Fossil vs. Molecular dates Cretaceous Paleogene Cretaceous Paleogene
- 29. Traditional vs. Molecular Cretaceous Paleogene 1:1 RSS 31269.3 Traditional approach Cretaceous Paleogene Meredith et al. 2011
- 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. Approach comparison Meredith Traditional et al. approach 2011 Modified Reis Hedman et al. approach 2012
- 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. 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. Conclusions • Novel fossil-only tree dating approach
- 35. Conclusions • Novel fossil-only tree dating approach • Mimics molecular approach
- 36. Conclusions • Novel fossil-only tree dating approach • Mimics molecular approach • Helps close molecule-fossil gap
- 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