Claddis: a new R package for
automating disparity analyses based
on cladistic datasets
Graeme T. Lloyd
Acknowledgements
Matt
Friedman
Roger
Benson
Liam
Revell
Mark
Bell
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
Cladistic
matrix
Distance
matrix
Ordination ‘Morphospace’
Cladistic disparity
Cladistic
matrix
Distance
matrix
Ordination ‘Morphospace’
Tree
Ancestral
states
‘Phylo-
Morphospace’
Claddis
Cladistic
matrix
Distance
matrix
Ordination ‘Morphospace’
Tree
Ancestral
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 001011
Taxon_j 101101
Taxon_i 001011
Taxon_j 101101
Wills et al. 1994
Distance
Ordered vs. Unordered
Gap-coding
Polymorphisms
Weighting
Missing data
Taxon_A 0000000000
Taxon_B 00000111??
Taxon_C 11????????
Taxon_D 00110?????
Taxon_E ?????01100
A B
A C
1.73
1...
Rescaled distances
Distance / N = Gower Dissimilarity
Distance / Max = MOD Dissimilarity
A B
A C
0.22
0.71
Gower
0.61
1.00...
Gower vs. MOD
Gower
Gower vs. MOD
PC2(16.0%)
PC1 (34.1%)
Gower
Gower vs. MOD
MOD
Gower vs. MOD
PC2(9.5%)
PC1 (14.1%)
MOD
Missing data
Taxon_A 0000000000
Taxon_B 00000111??
Taxon_C 11????????
Taxon_D 00110?????
Taxon_E ?????01100
D E ?
Euclidea...
Prune
Taxon_A 0000000000
Taxon_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. 20...
Phylogenetic prediction
Estimateallstates
Estimate tips
No Yes
NoYes
? ?
=
=
=
=
=
?
?
Phylogenetic prediction
Estimateallstates
Estimate tips
No Yes
NoYes
=
? ?
=
=
=
=
=
?
?
=
? ?
=
=
=
=
?
?
? ?
=
? ?
=
=
=
=
?
?
? ?
Phylogenetic prediction
Estimateallstates
Estimate tips
No Yes
NoYes
=
=
=
=
=
? ?
=
=
=
=
=
?
?
Phylogenetic prediction
Estimateallstates
Estimate tips
No Yes
NoYes
=
=
=
=
=
? ?
=
=
=
=
=
?
?
=
? ?
=
=
=
=
?
?
? ?
=
=...
Phylogenetic signal
Estimateallstates
Estimate tips
No Yes
NoYes
0.63
0.66
0.530.52
Ordination
N Y
N
Y
Tips
States
PC1
PC2
Ordination
N Y
N
Y
Tips
States
PC1
PC2
Ordination
N Y
N
Y
Tips
States
PC1
PC2
Ordination with ancestors
PC1
PC2
N Y
N
Y
Tips
States
Ordination with ancestors
N Y
N
Y
Tips
States
PC1
PC2
Ordination with ancestors
N Y
N
Y
Tips
States
PC1
PC2
Ordination with ancestors
N Y
N
Y
Tips
States
PC1
PC2
Ordination with ancestors
Phylogenetic distances
PC1
PC2
Disparity time series
Cladistic
matrix
Distance
matrix
Ordination ‘Morphospace’
Time
series
Disparity time series
Cladistic
matrix
Distance
matrix
Ordination ‘Morphospace’
Time
series
Time
series
Benson and Drucken...
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
States
Recommendations
MOD
N Y
N
Y
Tips
States
Ordination
Time
series
Distance
matrix
Time
series
✔
Recommendations
MOD
N Y
N
Y
Tips
States
Ordination
Time
series
Distance
matrix
Time
series
✔
Recommendations
MOD
N Y
N
Y
Tips
States
Ordination
Time
series
Distance
matrix
Time
series
✔
Use
!
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Claddis: a new R package for automating disparity analyses based on cladistic datasets

  1. 1. Claddis: a new R package for automating disparity analyses based on cladistic datasets Graeme T. Lloyd
  2. 2. Acknowledgements Matt Friedman Roger Benson Liam Revell Mark Bell
  3. 3. Extinction Random Marginal Asymmetric Korn et al. in press Intensity
  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 ‘Morphospace’ Tree Ancestral states ‘Phylo- Morphospace’
  9. 9. Claddis Cladistic matrix Distance matrix Ordination ‘Morphospace’ Tree Ancestral states ‘Phylo- Morphospace’ Inputs Outputs
  10. 10. Claddis Safe taxonomic reduction #NEXUS TNT Step matrices Continuous characters Other features Current limitations
  11. 11. Data Choiniere et al. in press
  12. 12. Data Choiniere et al. in press 114 taxa | 555 characters
  13. 13. Distance Taxon_i 001011 Taxon_j 101101 Taxon_i 001011 Taxon_j 101101 Wills et al. 1994
  14. 14. Distance Ordered vs. Unordered Gap-coding Polymorphisms Weighting
  15. 15. Missing data Taxon_A 0000000000 Taxon_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
  16. 16. Rescaled distances Distance / N = Gower Dissimilarity Distance / Max = MOD Dissimilarity A B A C 0.22 0.71 Gower 0.61 1.00 MOD
  17. 17. Gower vs. MOD Gower
  18. 18. Gower vs. MOD PC2(16.0%) PC1 (34.1%) Gower
  19. 19. Gower vs. MOD MOD
  20. 20. Gower vs. MOD PC2(9.5%) PC1 (14.1%) MOD
  21. 21. Missing data Taxon_A 0000000000 Taxon_B 00000111?? Taxon_C 11???????? Taxon_D 00110????? Taxon_E ?????01100 D E ? Euclidean 0 N 0 Max
  22. 22. Prune Taxon_A 0000000000 Taxon_B 00000111?? Taxon_C 11???????? Taxon_D 00110????? Taxon_E ?????01100
  23. 23. Fill gaps Butler et al. 2011 Average values: (Wills 1997) Phylogenetic prediction: (Brusatte et al. 2011; Butler et al. 2011)
  24. 24. Phylogenetic prediction Estimateallstates Estimate tips No Yes NoYes ? ? = = = = = ? ?
  25. 25. Phylogenetic prediction Estimateallstates Estimate tips No Yes NoYes = ? ? = = = = = ? ? = ? ? = = = = ? ? ? ?
  26. 26. = ? ? = = = = ? ? ? ? Phylogenetic prediction Estimateallstates Estimate tips No Yes NoYes = = = = = ? ? = = = = = ? ?
  27. 27. Phylogenetic prediction Estimateallstates Estimate tips No Yes NoYes = = = = = ? ? = = = = = ? ? = ? ? = = = = ? ? ? ? = = = = =
  28. 28. Phylogenetic signal Estimateallstates Estimate tips No Yes NoYes 0.63 0.66 0.530.52
  29. 29. Ordination N Y N Y Tips States PC1 PC2
  30. 30. Ordination N Y N Y Tips States PC1 PC2
  31. 31. Ordination N Y N Y Tips States PC1 PC2
  32. 32. Ordination with ancestors PC1 PC2 N Y N Y Tips States
  33. 33. Ordination with ancestors N Y N Y Tips States PC1 PC2
  34. 34. Ordination with ancestors N Y N Y Tips States PC1 PC2
  35. 35. Ordination with ancestors N Y N Y Tips States PC1 PC2
  36. 36. Ordination with ancestors Phylogenetic distances PC1 PC2
  37. 37. Disparity time series Cladistic matrix Distance matrix Ordination ‘Morphospace’ Time series
  38. 38. Disparity time series Cladistic matrix Distance matrix Ordination ‘Morphospace’ Time series Time series Benson and Druckenmiller in press
  39. 39. Disparity time series Tips only All nodes
  40. 40. Phylogenetic distance time series Tips only All nodes
  41. 41. Model residual time series Tips only Significantly +ve Significantly -ve
  42. 42. Model residual time series All nodes Significantly +ve
  43. 43. Recommendations MOD
  44. 44. Recommendations MOD N Y N Y Tips States
  45. 45. Recommendations MOD N Y N Y Tips States Ordination Time series Distance matrix Time series ✔
  46. 46. Recommendations MOD N Y N Y Tips States Ordination Time series Distance matrix Time series ✔
  47. 47. Recommendations MOD N Y N Y Tips States Ordination Time series Distance matrix Time series ✔ Use !

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