A new R package for automating cladistic ordination and the effects of phylogenetic signal on disparity measures
Upcoming SlideShare
Loading in...5
×

Like this? Share it with your network

Share
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Be the first to comment
    Be the first to like this
No Downloads

Views

Total Views
483
On Slideshare
459
From Embeds
24
Number of Embeds
1

Actions

Shares
Downloads
4
Comments
0
Likes
0

Embeds 24

https://twitter.com 24

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
    No notes for slide

Transcript

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