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A new R package for automating cladistic ordination and the effects of phylogenetic signal
on disparity measures
Graeme T. Lloyd
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Acknowledgements
Matt Friedman
Roger Benson
Liam Revell
MarkBell
PeterSmits
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Extinction
Random
Marginal
Asymmetric
Korn et al. in press
Intensity
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Clade comparison
Sidlauskis 2008
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Center of gravity
Hughes et al. 2013
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Caveat emptor
Anderson and Friedman 2012
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Cladistic disparity
Cladisticmatrix
Distancematrix Ordination ‘Morphospace’
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Cladistic disparity
Cladisticmatrix
Distancematrix Ordination ‘Morphospace’
TreeAncestral
states‘Phylo-
Morphospace’
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Claddis
Cladisticmatrix
Distancematrix Ordination ‘Morphospace’
TreeAncestral
states‘Phylo-
Morphospace’
Inputs Outputs
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Claddis
Safe taxonomic reduction
#NEXUS TNT Step matrices
Continuous characters
Other features Current limitations
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Data
Choiniere et al. in press
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Data
Choiniere et al. in press
114 taxa | 555 characters
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Distance
Ordered vs. Unordered
Gap-coding
Polymorphisms
Weighting
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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
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Rescaled distances
Distance / N = Gower Dissimilarity
Distance / Max = MOD Dissimilarity
A B
A C
0.22
0.71
Gower
0.61
1.00
MOD
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Gower vs. MOD
Gower
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Gower vs. MODPC
2
PC1
Gower
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Gower vs. MOD
MOD
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Gower vs. MODPC
2
PC1
MOD
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Missing data
Taxon_A 0000000000Taxon_B 00000111??Taxon_C 11????????Taxon_D 00110?????Taxon_E ?????01100
D E ?Euclidean
0N
0Max
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Prune
Taxon_A 0000000000Taxon_B 00000111??Taxon_C 11????????Taxon_D 00110?????
Taxon_E ?????01100
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Fill gaps
Butler et al. 2011
Average values:(Wills 1997)
Phylogenetic prediction:(Brusatte et al. 2011; Butler et al. 2011)
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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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=
? ?
=
=
=
=
?
?
? ?
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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Phylogenetic signalEs
timat
e al
l sta
tes
Estimate tipsNo Yes
No
Yes
0.63
0.66
0.530.52
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Ordination I
PC1
PC2
N YNY
Tips
Stat
es
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Ordination II
N YNY
Tips
Stat
es
PC1
PC2
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Ordination III
N YNY
Tips
Stat
es
PC1
PC2
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Ordination IV
N YNY
Tips
Stat
es
PC1
PC2
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Ordination V
Phylogenetic distances
PC1
PC2
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Conclusions
MOD
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Conclusions
MODN Y
N
Y
Tips
Stat
es
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Conclusions
MODN Y
N
Y
Tips
Stat
es