Automated generation of large phylogenies and a probabilistically time-scaled 1,000-taxon phylogenetic hypothesis for Mesozoic dinosaurs: dating the origins of flight and crown-birds

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This document discusses automated generation of large phylogenies and probabilistic time-scaling of a 1,000-taxon phylogenetic tree for Mesozoic dinosaurs. It examines dating the origins of flight and crown birds using two different time-scaling methods: cal3 and Hedman. The results show that crown birds likely originated between 80-90 million years ago according to both methods, though cal3 estimates a slightly narrower time range. The study provides new insights into the timing of key evolutionary transitions in dinosaurs.

Science

Automated generation of large phylogenies
and a probabilistically time-scaled 1,000-taxon
phylogenetic hypothesis for Mesozoic
dinosaurs: dating 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
Branch-sharing
Ruta et al 2006; Brusatte et al 2008
Arbitrary addition(s)
Derstler 1982
Minimum branch-length
Laurin 2004

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

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

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

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

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

Pipeline
Collect
data
Reconcile
taxonomy

Pipeline
Collect
data
Reconcile
taxonomy
Define
cutoff

Pipeline
Collect
data
Reconcile
taxonomy
Define
cutoff
Consensus
vs. MPTs

Taxonomy
tree
Pipeline
A
B
C
D
E
F
G
H
I
J
K
L
Class Order Family Genus

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

Taxonomy
tree
Safe Taxon.
Reduction
Weights
Pipeline

Taxonomy
tree
Safe Taxon.
Reduction
Weights Inference
Pipeline

Crown birds
cal3
Molecular Clock
Hedman
95% HPD

Crown birds
cal3
Molecular Clock
Hedman
Morphological Clock
95% HPD

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Automated generation of large phylogenies and a probabilistically time-scaled 1,000-taxon phylogenetic hypothesis for Mesozoic dinosaurs: dating the origins of flight and crown-birds

1. Automated generation of large phylogenies and a probabilistically time-scaled 1,000-taxon phylogenetic hypothesis for Mesozoic dinosaurs: dating 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 Branch-sharing Ruta et al 2006; Brusatte et al 2008 Arbitrary addition(s) Derstler 1982 Minimum branch-length Laurin 2004

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

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

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

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. Taxonomy tree Pipeline A B C D E F G H I J K L Class Order Family Genus

22. Taxonomy tree Safe Taxon. Reduction Pipeline 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 cal3Hedman

27. Dinosauria cal3Hedman

28. Dinosauria 2.6% 9.6% cal3Hedman

29. Dinosauria 0.2% 1.0% cal3Hedman -

30. Aves cal3Hedman

31. Aves cal3Hedman

32. Crown birds cal3Hedman

33. Crown birds cal3 Hedman 95% HPD

34. Crown birds cal3 Molecular Clock Hedman 95% HPD

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

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)

Automated generation of large phylogenies and a probabilistically time-scaled 1,000-taxon phylogenetic hypothesis for Mesozoic dinosaurs: dating the origins of flight and crown-birds

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Automated generation of large phylogenies and a probabilistically time-scaled 1,000-taxon phylogenetic hypothesis for Mesozoic dinosaurs: dating the origins of flight and crown-birds

Editor's Notes