A probabilistically time-scaled 1,000-taxon phylogenetic hypothesis for Mesozoic dinosaurs and the origins of flight and crown-birds

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This document describes a study that uses probabilistic time scaling methods to generate a 1,000-taxon phylogenetic tree for Mesozoic dinosaurs and the origins of flight and modern birds. It compares results from the Hedman and cal3 time scaling methods and finds broad agreement between the two, with dinosaurs originating in the Late Triassic, flight in the Late Jurassic, and modern birds in the Late Cretaceous.

Science

A probabilistically time-scaled 1,000-
taxon phylogenetic hypothesis for
Mesozoic dinosaurs and the origins
of flight and crown-birds
Graeme T. Lloyd David W. Bapst
@GraemeTLloyd @dwbapst
Katie E. Davis Matt Friedman
@drkatiedavis @Friedman_Lab

When?
1. Dinosaurs
2. Flight
3. Crown birds

A posteriori time-scaling
paleotree
strap

A posteriori time-scaling
Arbitrary
Arbitrary addition(s)
Derstler 1982
Minimum branch-length
Laurin 2004
Branch-sharing
Ruta et al 2006; Brusatte et al 2008

A posteriori time-scaling
Arbitrary Probabilistic
cal3
Bapst 2013
Nowak
Nowak et al 2013
Hedman method
Lloyd and Friedman in prep
Arbitrary addition(s)
Derstler 1982
Minimum branch-length
Laurin 2004
Branch-sharing
Ruta et al 2006; Brusatte et al 2008

A posteriori time-scaling
Arbitrary Probabilistic
cal3
Bapst 2013
Hedman method
Lloyd and Friedman in prep

cal3 method
*
*
*
*
* *
*
*
*
*
Bapst 2013

Hedman method
Target node Outgroup taxon
TIME
Hedman 2010; Lloyd and Friedman in prep

Phylogenetic approach
Pisani et al. 2002 Lloyd et al. 2008

Pipeline
Collect
data
Reconcile
taxonomy

Pipeline
Collect
data
Reconcile
taxonomy
Define
cutoff

Pipeline
Collect
data
Reconcile
taxonomy
Define
cutoff
Consensus
vs. MPTs

Pipeline
Taxonomy
tree
ABCDEFGHIJKL
Class Order Family Genus

Pipeline
Taxonomy
tree
Safe Taxon.
Reduction
github.com/graemetlloyd/Claddis
Wilkinson 1995

Taxonomy
tree
Safe Taxon.
Reduction
Weights
Pipeline

Taxonomy
tree
Safe Taxon.
Reduction
Weights Inference
Pipeline

Crown birds
cal3
Hedman
Molecular Clock
95% HPD

Crown birds
cal3
Hedman
Molecular Clock
95% HPD
Morphological Clock

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A probabilistically time-scaled 1,000-taxon phylogenetic hypothesis for Mesozoic dinosaurs and the origins of flight and crown-birds

1. A probabilistically time-scaled 1,000- taxon phylogenetic hypothesis for Mesozoic dinosaurs and the origins of flight and crown-birds Graeme T. Lloyd David W. Bapst @GraemeTLloyd @dwbapst Katie E. Davis Matt Friedman @drkatiedavis @Friedman_Lab

2. When? 1. Dinosaurs 2. Flight 3. Crown birds

3. Simultaneous inference Lee et al 2014

4. A posteriori time-scaling paleotree strap

5. A posteriori time-scaling + paleotree strap

6. A posteriori time-scaling + = paleotree strap

7. A posteriori time-scaling Arbitrary Arbitrary addition(s) Derstler 1982 Minimum branch-length Laurin 2004 Branch-sharing Ruta et al 2006; Brusatte et al 2008

8. A posteriori time-scaling Arbitrary Probabilistic cal3 Bapst 2013 Nowak Nowak et al 2013 Hedman method Lloyd and Friedman in prep Arbitrary addition(s) Derstler 1982 Minimum branch-length Laurin 2004 Branch-sharing Ruta et al 2006; Brusatte et al 2008

9. A posteriori time-scaling Arbitrary Probabilistic cal3 Bapst 2013 Hedman method Lloyd and Friedman in prep

10. cal3 method * * * * * * * * * * Bapst 2013

11. cal3 method * * * * * * * * * * Bapst 2013

12. cal3 method * * * * * * * * * * Bapst 2013

13. cal3 method * * * * * * * * * * Bapst 2013

14. Hedman method Target node Outgroup taxon TIME Hedman 2010; Lloyd and Friedman in prep

15. Hedman method Target node Outgroup taxon TIME Hedman 2010; Lloyd and Friedman in prep

16. Phylogenetic approach Pisani et al. 2002 Lloyd et al. 2008

17. Pipeline Collect data graemetlloyd.com

18. Pipeline Collect data Reconcile taxonomy

19. Pipeline Collect data Reconcile taxonomy Define cutoff

20. Pipeline Collect data Reconcile taxonomy Define cutoff Consensus vs. MPTs

21. Pipeline Taxonomy tree ABCDEFGHIJKL Class Order Family Genus

22. Pipeline Taxonomy tree Safe Taxon. Reduction github.com/graemetlloyd/Claddis Wilkinson 1995

23. Taxonomy tree Safe Taxon. Reduction Weights Pipeline

24. Taxonomy tree Safe Taxon. Reduction Weights Inference Pipeline

25. Taxonomy tree Safe Taxon. Reduction Weights Inference Pipeline

26. Results Hedman cal3

27. Dinosauria Hedman cal3

28. Dinosauria 2.6% 9.6% Hedman cal3

29. Dinosauria 0.2% 1.0% Hedman cal3 -

30. Aves Hedman cal3

31. Aves Hedman cal3

32. Crown birds Hedman cal3

33. Crown birds cal3 Hedman 95% HPD

34. Crown birds cal3 Hedman Molecular Clock 95% HPD

35. Crown birds cal3 Hedman Molecular Clock 95% HPD Morphological Clock

36. Conclusions Hedman cal3

37. Conclusions Hedman cal3

38. Conclusions Hedman cal3

39. Conclusions Hedman cal3

Editor's Notes

Ca3 dates: 243.2802 252.1859 247.3917 Hedman dates: 245.4865 255.4662 249.4067
Ca3 dates: 243.2802 252.1859 247.3917 Hedman dates: 245.4865 255.4662 249.4067
Ca3 dates: 236.4024 248.3425 240.9010 Hedman dates: 235.9872 249.7923 243.3357
Cal3 dates: 155.7618 168.0976 163.1616 (155.7546 168.2523 163.0148) Hedman dates: 152.3904 172.6907 158.1100 (152.3904 172.6907 157.9058)
Cal3 dates: 151.2605 165.8007 160.2343 (150.8128 165.7816 160.0459) Hedman dates: 152.0843 171.7647 157.4884 (152.0914 171.3843 157.4510)
Cal3 dates: 70.48813 95.94979 76.62220 (70.70868 94.13697 76.29693) Hedman dates: 68.98936 108.00520 86.01446 (69.07435 108.55864 86.10264)

A probabilistically time-scaled 1,000-taxon phylogenetic hypothesis for Mesozoic dinosaurs and the origins of flight and crown-birds

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A probabilistically time-scaled 1,000-taxon phylogenetic hypothesis for Mesozoic dinosaurs and the origins of flight and crown-birds

Editor's Notes