claddis: a new r package for automating disparity analyses based on cladistic datasets
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Claddis: a new R package for automating disparity analyses based on cladistic datasets
Graeme T. Lloyd
Acknowledgements
Matt Friedman
Roger Benson
Liam Revell
MarkBell
Extinction
Random
Marginal
Asymmetric
Korn et al. in press
Intensity
Clade comparison
Sidlauskis 2008
Center of gravity
Hughes et al. 2013
Caveat emptor
Anderson and Friedman 2012
Cladistic disparity
Cladisticmatrix
Distancematrix Ordination ‘Morphospace’
Cladistic disparity
Cladisticmatrix
Distancematrix Ordination ‘Morphospace’
TreeAncestral
states‘Phylo-
Morphospace’
Claddis
Cladisticmatrix
Distancematrix Ordination ‘Morphospace’
TreeAncestral
states‘Phylo-
Morphospace’
Inputs Outputs
Claddis
Safe taxonomic reduction
#NEXUS TNT Step matrices
Continuous characters
Other features Current limitations
Data
Choiniere et al. in press
Data
Choiniere et al. in press
114 taxa | 555 characters
Distance
Taxon_i 001011Taxon_j 101101
Taxon_i 001011Taxon_j 101101
Wills et al. 1994
Distance
Ordered vs. Unordered
Gap-coding
Polymorphisms
Weighting
Missing data
Taxon_A 0000000000Taxon_B 00000111??Taxon_C 11????????Taxon_D 00110?????Taxon_E ?????01100
A B
A C
1.73
1.41
Euclidean
8
2
N
2.83
1.41
Max
Rescaled distances
Distance / N = Gower Dissimilarity
Distance / Max = MOD Dissimilarity
A B
A C
0.22
0.71
Gower
0.61
1.00
MOD
Gower vs. MOD
Gower
Gower vs. MODPC
2 (1
6.0%
)
PC1 (34.1%)
Gower
Gower vs. MOD
MOD
Gower vs. MODPC
2 (9
.5%
)
PC1 (14.1%)
MOD
Missing data
Taxon_A 0000000000Taxon_B 00000111??Taxon_C 11????????Taxon_D 00110?????Taxon_E ?????01100
D E ?Euclidean
0N
0Max
Prune
Taxon_A 0000000000Taxon_B 00000111??Taxon_C 11????????Taxon_D 00110?????
Taxon_E ?????01100
Fill gaps
Butler et al. 2011
Average values:(Wills 1997)
Phylogenetic prediction:(Brusatte et al. 2011; Butler et al. 2011)
Phylogenetic predictionEs
timat
e al
l sta
tes
Estimate tipsNo Yes
No
Yes
? ?
=
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Phylogenetic predictionEs
timat
e al
l sta
tes
Estimate tipsNo Yes
No
Yes
=
? ?
=
=
=
=
=
?
?
=
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=
=
=
=
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=
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=
=
=
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Phylogenetic predictionEs
timat
e al
l sta
tes
Estimate tipsNo Yes
No
Yes
=
=
=
=
=
? ?
=
=
=
=
=
?
?
Phylogenetic predictionEs
timat
e al
l sta
tes
Estimate tipsNo Yes
No
Yes
=
=
=
=
=
? ?
=
=
=
=
=
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?
=
? ?
=
=
=
=
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?
? ?
=
=
=
=
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Phylogenetic signalEs
timat
e al
l sta
tes
Estimate tipsNo Yes
No
Yes
0.63
0.66
0.530.52
Ordination
N YNY
Tips
Stat
es
PC1
PC2
Ordination
N YNY
Tips
Stat
es
PC1
PC2
Ordination
N YNY
Tips
Stat
es
PC1
PC2
Ordination with ancestors
PC1
PC2
N YNY
Tips
Stat
es
Ordination with ancestors
N YNY
Tips
Stat
es
PC1
PC2
Ordination with ancestors
N YNY
Tips
Stat
es
PC1
PC2
Ordination with ancestors
N YNY
Tips
Stat
es
PC1
PC2
Ordination with ancestors
Phylogenetic distances
PC1
PC2
Disparity time series
Cladisticmatrix
Distancematrix Ordination ‘Morphospace’
Timeseries
Disparity time series
Cladisticmatrix
Distancematrix Ordination ‘Morphospace’
Timeseries
Timeseries
Benson and Druckenmiller in press
Disparity time series
Tips only
All nodes
Phylogenetic distance time series
Tips only
All nodes
Model residual time series
Tips only
Significantly +ve
Significantly -ve
Model residual time series
All nodes
Significantly +ve
Recommendations
MOD
Recommendations
MOD
N Y
N
Y
Tips
Stat
es
Recommendations
MOD
N Y
N
Y
Tips
Stat
es
Ordination
Timeseries
Distancematrix
Timeseries
✔
Recommendations
MOD
N Y
N
Y
Tips
Stat
es
Ordination
Timeseries
Distancematrix
Timeseries
✔
Recommendations
MOD
N Y
N
Y
Tips
Stat
es
Ordination
Timeseries
Distancematrix
Timeseries
✔Use
!