measuring morphological diversity and tempo using discrete characters: advantages and disadvantages...
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Measuring morphological diversity and tempo using discrete characters: advantages and disadvantages of
including additional phylogenetic information
Graeme T. Lloyd @GraemeTLloyd
Acknowledgements
Emma SherrattThomas Guillerme
Discrete morphology
Discrete morphology
Discrete morphology
?
Discrete morphology
Discrete morphology
Discrete morphology
github.com/graemetlloyd/Claddis
Claddis
Lloyd 2016
github.com/graemetlloyd/Claddis
Claddis
Lloyd 2016
github.com/graemetlloyd/Claddis
Claddis
Lloyd 2016
github.com/graemetlloyd/Claddis
Claddis
Lloyd 2016
STR
github.com/graemetlloyd/Claddis
Claddis
Lloyd 2016
STR
#NEXUS
TNT/Hennig86
Claddis
Claddis
?
Claddis
(01)?
Claddis
(01)
0 1 2
1
1
?
Claddis
(01)
0 1 2
1
1
?
Outline
Phylogeny and disparity
Phylogeny and disparity
Increase sample size
Brusatte et al 2011
Phylogeny and disparity
Increase sample size Estimate missing states
Brusatte et al 2011; Butler et al 2011
Phylogeny and disparity
Increase sample size Estimate missing states
Brusatte et al 2011; Butler et al 2011; Hopkins and Smith 2015
Create phylomorphospace
Two phylomorphospace types
Two phylomorphospace types
Two phylomorphospace types
Brusatte et al 2011; Butler et al 2011
Two phylomorphospace types
Brusatte et al 2011; Butler et al 2011
Two phylomorphospace types
Brusatte et al 2011; Butler et al 2011; Hopkins and Smith 2015
Two phylomorphospace types
Two phylomorphospace types
Estim
ate
tip st
ates
Estimate all ancestral statesN Y
NY
Two phylomorphospace types
Estim
ate
tip st
ates
Estimate all ancestral statesN Y
NY
Two phylomorphospace types
Estim
ate
tip st
ates
Estimate all ancestral statesN Y
NY
Questions
Questions
How do phylomorphospace choices affect our inferences?To what degree are we measuring phylogenetic rather than
morphological signal?
Questions
How do phylomorphospace choices affect our inferences?To what degree are we measuring phylogenetic rather than
morphological signal?
Disparity dataset
152 taxa | 853 characters
Disparity dataset
Results: layout
N Y
NY
N Y
NY
N Y
NY
N Y
NY
Results: scree plots
Lloyd in prep
Results: visualisation
Lloyd in prep
r = 0.188
r = 0.204
r = 0.354
r = 0.653
r = 0.396
r = 0.841
Results: phylogenetic correlation
Lloyd in prep
Results: root distance
Lloyd in prep
Results: root distance rate
Lloyd in prep
Rate equations
Rate equations
𝑅𝑎𝑡𝑒=h𝐶 𝑎𝑛𝑔𝑒𝑇𝑖𝑚𝑒
Rate equations
𝑅𝑎𝑡𝑒=h𝐶 𝑎𝑛𝑔𝑒𝑇𝑖𝑚𝑒
𝑅𝑎𝑡𝑒=h𝐶 𝑎𝑛𝑔𝑒
𝑇𝑖𝑚𝑒×𝐶𝑜𝑚𝑝𝑙𝑒𝑡𝑒𝑛𝑒𝑠𝑠
Rate questions
Rate questions
Rate questions
Rate questions
Rate questions
Rate questions
Rate questions
Time
Rate questions
Time Change
Rate questions
Time Change
Completeness
Rate time series
Rate time series
Ruta et al 2006
Branches binned(Time)
Rate time series
Ruta et al 2006; Lloyd et al 2012
Stochastic changes(Change)
Branches binned(Time)
Rate time series
Ruta et al 2006; Lloyd et al 2012; Close et al 2015
Stochastic changes(Change)
Branches binned(Time)
Weighted average(Completeness)
Questions
Questions
How does ASR choice affect rate time series?How does correcting for completeness affect rate time series?
Questions
How does ASR choice affect rate time series?How does correcting for completeness affect rate time series?
Rate dataset
86 taxa | 91 characters
Rate dataset
Westoll 1949
Rate results
Rate resultsACCTRAN DELTRAN Likelihood Likelihood
+ Corr. 1Likelihood+ Corr. 2
Rate resultsACCTRAN DELTRAN Likelihood Likelihood
+ Corr. 1Likelihood+ Corr. 2
Lloydet al2012
Lloydet al2012
Brusatteet al2014
Closeet al2015
Lloyd2016
Rate resultsACCTRAN DELTRAN Likelihood Likelihood
+ Corr. 1Likelihood+ Corr. 2
Lloydet al2012
Lloydet al2012
Brusatteet al2014
Closeet al2015
Lloyd2016
Rate resultsACCTRAN DELTRAN Likelihood Likelihood
+ Corr. 1Likelihood+ Corr. 2
Lloydet al2012
Lloydet al2012
Brusatteet al2014
Closeet al2015
Lloyd2016
Rate resultsACCTRAN DELTRAN Likelihood Likelihood
+ Corr. 1Likelihood+ Corr. 2
1.39 1.77 0.78 0.23 0.78
Lloydet al2012
Lloydet al2012
Brusatteet al2014
Closeet al2015
Lloyd2016
Wobble index:
Conclusions
Conclusions
Conclusions
Conclusions
1.77
0.78
Conclusions
1.77
0.78