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-birdsGraeme T. Lloyd David W. Bapst

@GraemeTLloyd @dwbapstKatie E. Davis Matt Friedman

@drkatiedavis @Friedman_Lab

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-sharingRuta et al 2006; Brusatte et al 2008

Arbitrary addition(s)Derstler 1982

Minimum branch-lengthLaurin 2004

A posteriori time-scaling

cal3Bapst 2013

Hedman methodLloyd and Friedman in prep

NowakNowak et al 2013

Arbitrary Probabilistic

Branch-sharingRuta et al 2006; Brusatte et al 2008

Arbitrary addition(s)Derstler 1982

Minimum branch-lengthLaurin 2004

A posteriori time-scaling

cal3Bapst 2013

Hedman methodLloyd 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

TIM

E

Hedman 2010; Lloyd and Friedman in prep

Hedman method

Target node Outgroup taxon

TIM

E

Hedman 2010; Lloyd and Friedman in prep

Lloyd et al. 2008Pisani et al. 2002

Phylogenetic approach

Pipeline

Collectdata

graemetlloyd.com

Pipeline

Collectdata

Reconciletaxonomy

Pipeline

Collectdata

Reconciletaxonomy

Definecutoff

Pipeline

Collectdata

Reconciletaxonomy

Definecutoff

Consensusvs. MPTs

Taxonomytree

Pipeline

ABCDEFGHIJKL

Class Order Family Genus

Taxonomytree

Safe Taxon.Reduction

Pipeline

github.com/graemetlloyd/Claddis

Wilkinson 1995

Taxonomytree

Safe Taxon.Reduction Weights

Pipeline

Taxonomytree

Safe Taxon.Reduction Weights Inference

Pipeline

Taxonomytree

Safe Taxon.Reduction Weights Inference

Pipeline

Resultsca

l3H

edm

an

Dinosauriaca

l3H

edm

an

Dinosauria

2.6%

9.6%

cal3

Hed

man

Dinosauria

0.2%

1.0%

cal3

Hed

man

-

Avesca

l3H

edm

an

Avesca

l3H

edm

an

Crown birdsca

l3H

edm

an

Crown birds

cal3Hedman

95% HPD

Crown birds

cal3

Molecular Clock

Hedman95% HPD

Crown birds

cal3

Molecular Clock

Hedman

Morphological Clock

95% HPD

Conclusions

Hedman

cal3

Conclusions

Hedman

cal3

Conclusions

Hedman

cal3

Conclusions

Hedman

cal3