Post on 25-Jul-2015
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