A new R package for automating cladistic ordination and the effects of phylogenetic signal on disparity measures
Download as PPTX, PDF1 like1,510 views
1) The document describes a new R package called Claddis that performs cladistic ordination and accounts for phylogenetic signal when measuring morphological disparity. 2) Claddis takes cladistic data and phylogenetic trees as inputs and outputs ordinations of taxa in morphospace with and without consideration of ancestral state estimation. 3) The document demonstrates how accounting for phylogenetic relationships and estimating ancestral character states using Claddis affects ordination of morphological data and conclusions about disparity through several examples.
A new R package for automating cladistic ordination and the effects of phylogenetic signal on disparity measures
- 1. A new R package for automating cladistic ordination and the effects of phylogenetic signal on disparity measures Graeme T. Lloyd
- 5. Center of gravity Hughes et al. 2013
- 6. Caveat emptor Anderson and Friedman 2012
- 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
- 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
- 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
- 33. Conclusions MOD