Confidence intervals on node age estimates in vertebrate phylogeny
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This document presents a novel approach for dating trees using only fossil data that mimics molecular dating approaches. It modifies an existing method to account for uncertainty in node ages. This new fossil-only approach generates dates that more closely match molecular timescales than traditional methods. It has implications for improving estimates of phylogenetic diversity, extinction rates, evolutionary rates, trait models, and calibration distributions.
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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