A new R package for automating
cladistic ordination and the effects
of phylogenetic signal on disparity
measures
Graeme T....
Acknowledgements

Mark
Bell

Roger
Benson

Matt
Friedman

Liam
Revell

Peter
Smits
Extinction
Intensity

Random

Marginal

Asymmetric
Korn et al. in press
Clade comparison

Sidlauskis 2008
Center of gravity

Hughes et al. 2013
Caveat emptor

Anderson and Friedman 2012
Cladistic disparity

Cladistic
matrix

Distance
matrix

Ordination

‘Morphospace’
Cladistic disparity

Cladistic
matrix

Distance
matrix

Ordination

Tree

Ancestral
states

‘PhyloMorphospace’

‘Morphospa...
Claddis
Inputs

Outputs

Cladistic
matrix

Distance
matrix

Ordination

Tree

Ancestral
states

‘PhyloMorphospace’

‘Morph...
Claddis
Other features

Current limitations

Safe taxonomic reduction

Continuous characters

#NEXUS

TNT

Step matrices
Data

Choiniere et al. in press
Data
114 taxa | 555 characters

Choiniere et al. in press
Distance
Ordered vs. Unordered
Gap-coding
Polymorphisms
Weighting
Missing data
Taxon_A
Taxon_B
Taxon_C
Taxon_D
Taxon_E

0000000000
00000111??
11????????
00110?????
?????01100

Euclidean

N...
Rescaled distances
Distance / N = Gower Dissimilarity
Distance / Max = MOD Dissimilarity
Gower

MOD

A

B

0.22

0.61

A

...
Gower vs. MOD
Gower
Gower vs. MOD

PC2

Gower

PC1
Gower vs. MOD
MOD
Gower vs. MOD

PC2

MOD

PC1
Missing data
Taxon_A
Taxon_B
Taxon_C
Taxon_D
Taxon_E

0000000000
00000111??
11????????
00110?????
?????01100

Euclidean

D...
Prune
Taxon_A
Taxon_B
Taxon_C
Taxon_D

0000000000
00000111??
11????????
00110?????

Taxon_E ?????01100
Fill gaps

Average values:
(Wills 1997)

Phylogenetic prediction:
(Brusatte et al. 2011; Butler et al. 2011)
Butler et al....
Phylogenetic prediction
Estimate tips

No

?

=

Yes

Estimate all states

No

?

=
= ?

=
= ?

Yes
Phylogenetic prediction
Estimate tips

No

?
?

?

=

Yes

Estimate all states

No

?

=

Yes

=
= ?

?
?

=
= ?
=

=
= ?
...
Phylogenetic prediction
Estimate tips

No

?
?

?

=

=
= ?

Yes

Estimate all states

No

?

=

Yes

=

=

?
?

=
= ?
=

...
Phylogenetic prediction
Estimate tips

No

?
?

?

=

=
= ?

Yes

Estimate all states

No

?

=

Yes

=

=

?
?

=
= ?
=

...
Phylogenetic signal
Estimate tips

Yes

0.52

0.53
0.66

Yes

Estimate all states

No

No

0.63
Ordination I
Tips

PC2

States

N Y

PC1

N
Y
Ordination II
Tips

PC2

States

N Y

PC1

N
Y
Ordination III
Tips

N
Y

PC2

States

N Y

PC1
PC2

Ordination IV

Tips
States

N Y
N
Y

PC1
Ordination V

PC2

Phylogenetic distances

PC1
Conclusions
MOD
Conclusions
MOD

Tips

States

N
N
Y

Y
Conclusions
MOD

Tips

States

N
N
Y

Y
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A new R package for automating cladistic ordination and the effects of phylogenetic signal on disparity measures

  1. 1. A new R package for automating cladistic ordination and the effects of phylogenetic signal on disparity measures Graeme T. Lloyd
  2. 2. Acknowledgements Mark Bell Roger Benson Matt Friedman Liam Revell Peter Smits
  3. 3. Extinction Intensity Random Marginal Asymmetric Korn et al. in press
  4. 4. Clade comparison Sidlauskis 2008
  5. 5. Center of gravity Hughes et al. 2013
  6. 6. Caveat emptor Anderson and Friedman 2012
  7. 7. Cladistic disparity Cladistic matrix Distance matrix Ordination ‘Morphospace’
  8. 8. Cladistic disparity Cladistic matrix Distance matrix Ordination Tree Ancestral states ‘PhyloMorphospace’ ‘Morphospace’
  9. 9. Claddis Inputs Outputs Cladistic matrix Distance matrix Ordination Tree Ancestral states ‘PhyloMorphospace’ ‘Morphospace’
  10. 10. Claddis Other features Current limitations Safe taxonomic reduction Continuous characters #NEXUS TNT Step matrices
  11. 11. Data Choiniere et al. in press
  12. 12. Data 114 taxa | 555 characters Choiniere et al. in press
  13. 13. Distance Ordered vs. Unordered Gap-coding Polymorphisms Weighting
  14. 14. Missing data Taxon_A Taxon_B Taxon_C Taxon_D Taxon_E 0000000000 00000111?? 11???????? 00110????? ?????01100 Euclidean N Max A B 1.73 8 2.83 A C 1.41 2 1.41
  15. 15. Rescaled distances Distance / N = Gower Dissimilarity Distance / Max = MOD Dissimilarity Gower MOD A B 0.22 0.61 A C 0.71 1.00
  16. 16. Gower vs. MOD Gower
  17. 17. Gower vs. MOD PC2 Gower PC1
  18. 18. Gower vs. MOD MOD
  19. 19. Gower vs. MOD PC2 MOD PC1
  20. 20. Missing data Taxon_A Taxon_B Taxon_C Taxon_D Taxon_E 0000000000 00000111?? 11???????? 00110????? ?????01100 Euclidean D E N Max ? 0 0
  21. 21. Prune Taxon_A Taxon_B Taxon_C Taxon_D 0000000000 00000111?? 11???????? 00110????? Taxon_E ?????01100
  22. 22. Fill gaps Average values: (Wills 1997) Phylogenetic prediction: (Brusatte et al. 2011; Butler et al. 2011) Butler et al. 2011
  23. 23. Phylogenetic prediction Estimate tips No ? = Yes Estimate all states No ? = = ? = = ? Yes
  24. 24. Phylogenetic prediction Estimate tips No ? ? ? = Yes Estimate all states No ? = Yes = = ? ? ? = = ? = = = ? = = ?
  25. 25. Phylogenetic prediction Estimate tips No ? ? ? = = = ? Yes Estimate all states No ? = Yes = = ? ? = = ? = = = = = ? = = ?
  26. 26. Phylogenetic prediction Estimate tips No ? ? ? = = = ? Yes Estimate all states No ? = Yes = = ? ? = = ? = = = = ? = = = = = = ? = =
  27. 27. Phylogenetic signal Estimate tips Yes 0.52 0.53 0.66 Yes Estimate all states No No 0.63
  28. 28. Ordination I Tips PC2 States N Y PC1 N Y
  29. 29. Ordination II Tips PC2 States N Y PC1 N Y
  30. 30. Ordination III Tips N Y PC2 States N Y PC1
  31. 31. PC2 Ordination IV Tips States N Y N Y PC1
  32. 32. Ordination V PC2 Phylogenetic distances PC1
  33. 33. Conclusions MOD
  34. 34. Conclusions MOD Tips States N N Y Y
  35. 35. Conclusions MOD Tips States N N Y Y

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