a new r package for automating cladistic ordination and the effects of phylogenetic signal on...
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A new R package for automating cladistic ordination and the effects of phylogenetic signal
on disparity measures
Graeme T. Lloyd
Acknowledgements
Matt Friedman
Roger Benson
Liam Revell
MarkBell
PeterSmits
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
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
PC1
Gower
Gower vs. MOD
MOD
Gower vs. MODPC
2
PC1
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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?
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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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?
? ?
=
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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 I
PC1
PC2
N YNY
Tips
Stat
es
Ordination II
N YNY
Tips
Stat
es
PC1
PC2
Ordination III
N YNY
Tips
Stat
es
PC1
PC2
Ordination IV
N YNY
Tips
Stat
es
PC1
PC2
Ordination V
Phylogenetic distances
PC1
PC2
Conclusions
MOD
Conclusions
MODN Y
N
Y
Tips
Stat
es
Conclusions
MODN Y
N
Y
Tips
Stat
es