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Automated generation of large phylogenies
and a probabilistically time-scaled 1,000-taxon
phylogenetic hypothesis for Meso...
When?
1. Dinosaurs
2. Flight
3. Crown birds
Simultaneous inference
Lee et al 2014
A posteriori time-scaling
paleotree
strap
A posteriori time-scaling
+
paleotree
strap
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 198...
A posteriori time-scaling
cal3
Bapst 2013
Hedman method
Lloyd and Friedman in prep
Nowak
Nowak et al 2013
Arbitrary Probab...
A posteriori time-scaling
cal3
Bapst 2013
Hedman method
Lloyd and Friedman in prep
Arbitrary Probabilistic
cal3 method
*
*
*
*
**
*
*
*
*
Bapst 2013
cal3 method
*
*
*
*
**
*
*
*
*
Bapst 2013
cal3 method
*
*
*
*
**
*
*
*
*
Bapst 2013
cal3 method
*
*
*
*
**
*
*
*
*
Bapst 2013
Hedman method
Target node Outgroup taxon
TIME
Hedman 2010; Lloyd and Friedman in prep
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
graemetlloyd.com
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
Taxonomy
tree
Safe Taxon.
Reduction
Weights Inference
Pipeline
Results
cal3Hedman
Dinosauria
cal3Hedman
Dinosauria
2.6%
9.6%
cal3Hedman
Dinosauria
0.2%
1.0%
cal3Hedman
-
Aves
cal3Hedman
Aves
cal3Hedman
Crown birds
cal3Hedman
Crown birds
cal3
Hedman
95% HPD
Crown birds
cal3
Molecular Clock
Hedman
95% HPD
Crown birds
cal3
Molecular Clock
Hedman
Morphological Clock
95% HPD
Conclusions
Hedman
cal3
Conclusions
Hedman
cal3
Conclusions
Hedman
cal3
Conclusions
Hedman
cal3
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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

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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. 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. 2. When? 1. Dinosaurs 2. Flight 3. Crown birds
  3. 3. Simultaneous inference Lee et al 2014
  4. 4. A posteriori time-scaling paleotree strap
  5. 5. A posteriori time-scaling + paleotree strap
  6. 6. A posteriori time-scaling + = paleotree strap
  7. 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. 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. 9. A posteriori time-scaling cal3 Bapst 2013 Hedman method Lloyd and Friedman in prep Arbitrary Probabilistic
  10. 10. cal3 method * * * * ** * * * * Bapst 2013
  11. 11. cal3 method * * * * ** * * * * Bapst 2013
  12. 12. cal3 method * * * * ** * * * * Bapst 2013
  13. 13. cal3 method * * * * ** * * * * Bapst 2013
  14. 14. Hedman method Target node Outgroup taxon TIME Hedman 2010; Lloyd and Friedman in prep
  15. 15. Hedman method Target node Outgroup taxon TIME Hedman 2010; Lloyd and Friedman in prep
  16. 16. Lloyd et al. 2008Pisani et al. 2002 Phylogenetic approach
  17. 17. Pipeline Collect data graemetlloyd.com
  18. 18. Pipeline Collect data Reconcile taxonomy
  19. 19. Pipeline Collect data Reconcile taxonomy Define cutoff
  20. 20. Pipeline Collect data Reconcile taxonomy Define cutoff Consensus vs. MPTs
  21. 21. Taxonomy tree Pipeline A B C D E F G H I J K L Class Order Family Genus
  22. 22. Taxonomy tree Safe Taxon. Reduction Pipeline github.com/graemetlloyd/Claddis Wilkinson 1995
  23. 23. Taxonomy tree Safe Taxon. Reduction Weights Pipeline
  24. 24. Taxonomy tree Safe Taxon. Reduction Weights Inference Pipeline
  25. 25. Taxonomy tree Safe Taxon. Reduction Weights Inference Pipeline
  26. 26. Results cal3Hedman
  27. 27. Dinosauria cal3Hedman
  28. 28. Dinosauria 2.6% 9.6% cal3Hedman
  29. 29. Dinosauria 0.2% 1.0% cal3Hedman -
  30. 30. Aves cal3Hedman
  31. 31. Aves cal3Hedman
  32. 32. Crown birds cal3Hedman
  33. 33. Crown birds cal3 Hedman 95% HPD
  34. 34. Crown birds cal3 Molecular Clock Hedman 95% HPD
  35. 35. Crown birds cal3 Molecular Clock Hedman Morphological Clock 95% HPD
  36. 36. Conclusions Hedman cal3
  37. 37. Conclusions Hedman cal3
  38. 38. Conclusions Hedman cal3
  39. 39. Conclusions Hedman cal3

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