lloydshort-141107031311-conversion-gate02.pdf

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Time scaling trees

Educação

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
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. 2008
Pisani 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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lloydshort-141107031311-conversion-gate02.pdf

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 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. 2008 Pisani 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