lloydshort-141107031311-conversion-gate02.pdf

lloydshort-141107031311-conversion-gate02.pdf
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
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 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
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. 2008 Pisani 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 cal3 Hedman
Dinosauria cal3 Hedman
Dinosauria 2.6% 9.6% cal3 Hedman
Dinosauria 0.2% 1.0% cal3 Hedman -
Aves cal3 Hedman
Aves cal3 Hedman
Crown birds cal3 Hedman
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

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lloydshort-141107031311-conversion-gate02.pdf