Measuring morphological diversity and tempo using discrete characters: advantages and disadvantages of including additional phylogenetic information
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This document discusses measuring morphological diversity and rates of evolution using discrete character data from phylogenies. It compares approaches that consider only tip states versus those that estimate all ancestral states, and whether accounting for phylogenetic signal and character completeness affects inferences about disparity and evolutionary rates through time. Results show that the choice of ancestral state reconstruction method and accounting for completeness can significantly impact inferred disparity, phylogenetic signal, and inferred evolutionary rates through time.
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Measuring morphological diversity and tempo using discrete characters: advantages and disadvantages of including additional phylogenetic information
- 1. Measuring morphological diversity and tempo using discrete characters: advantages and disadvantages of including additional phylogenetic information Graeme T. Lloyd @GraemeTLloyd
- 14. Claddis
- 15. Claddis ?
- 16. Claddis (01)?
- 19. Outline
- 22. Phylogeny and disparity Increase sample size Brusatte et al 2011
- 23. Phylogeny and disparity Increase sample size Estimate missing states Brusatte et al 2011; Butler et al 2011
- 24. Phylogeny and disparity Increase sample size Estimate missing states Brusatte et al 2011; Butler et al 2011; Hopkins and Smith 2015 Create phylomorphospace
- 27. Two phylomorphospace types Brusatte et al 2011; Butler et al 2011
- 28. Two phylomorphospace types Brusatte et al 2011; Butler et al 2011
- 29. Two phylomorphospace types Brusatte et al 2011; Butler et al 2011; Hopkins and Smith 2015
- 31. Two phylomorphospace types Estimatetipstates Estimate all ancestral states N Y NY
- 32. Two phylomorphospace types Estimatetipstates Estimate all ancestral states N Y NY
- 33. Two phylomorphospace types Estimatetipstates Estimate all ancestral states N Y NY
- 34. Questions
- 35. Questions How do phylomorphospace choices affect our inferences? To what degree are we measuring phylogenetic rather than morphological signal?
- 36. Questions How do phylomorphospace choices affect our inferences? To what degree are we measuring phylogenetic rather than morphological signal?
- 37. Disparity dataset 152 taxa | 853 characters
- 39. Results: layout N Y NY N Y NY N Y NY N Y NY
- 40. Results: scree plots Lloyd in prep
- 41. Results: visualisation Lloyd in prep
- 42. r = 0.188 r = 0.204 r = 0.354 r = 0.653 r = 0.396 r = 0.841 Results: phylogenetic correlation Lloyd in prep
- 43. Results: root distance Lloyd in prep
- 44. Results: root distance rate Lloyd in prep
- 46. Rate equations
- 48. Rate equations 𝑅𝑎𝑡𝑒 = 𝐶ℎ𝑎𝑛𝑔𝑒 𝑇𝑖𝑚𝑒 𝑅𝑎𝑡𝑒 = 𝐶ℎ𝑎𝑛𝑔𝑒 𝑇𝑖𝑚𝑒 × 𝐶𝑜𝑚𝑝𝑙𝑒𝑡𝑒𝑛𝑒𝑠𝑠
- 49. Rate questions
- 50. Rate questions
- 51. Rate questions
- 52. Rate questions
- 53. Rate questions
- 54. Rate questions
- 58. Rate time series
- 59. Rate time series Ruta et al 2006 Branches binned (Time)
- 60. Rate time series Ruta et al 2006; Lloyd et al 2012 Stochastic changes (Change) Branches binned (Time)
- 61. Rate time series Ruta et al 2006; Lloyd et al 2012; Close et al 2015 Stochastic changes (Change) Branches binned (Time) Weighted average (Completeness)
- 62. Questions
- 63. Questions How does ASR choice affect rate time series? How does correcting for completeness affect rate time series?
- 64. Questions How does ASR choice affect rate time series? How does correcting for completeness affect rate time series?
- 65. Rate dataset 86 taxa | 91 characters
- 67. Rate results
- 68. Rate results ACCTRAN DELTRAN Likelihood Likelihood + Corr. 1 Likelihood + Corr. 2
- 69. Rate results ACCTRAN DELTRAN Likelihood Likelihood + Corr. 1 Likelihood + Corr. 2 Lloyd et al 2012 Lloyd et al 2012 Brusatte et al 2014 Close et al 2015 Lloyd 2016
- 70. Rate results ACCTRAN DELTRAN Likelihood Likelihood + Corr. 1 Likelihood + Corr. 2 Lloyd et al 2012 Lloyd et al 2012 Brusatte et al 2014 Close et al 2015 Lloyd 2016
- 71. Rate results ACCTRAN DELTRAN Likelihood Likelihood + Corr. 1 Likelihood + Corr. 2 Lloyd et al 2012 Lloyd et al 2012 Brusatte et al 2014 Close et al 2015 Lloyd 2016
- 72. Rate results ACCTRAN DELTRAN Likelihood Likelihood + Corr. 1 Likelihood + Corr. 2 1.39 1.77 0.78 0.23 0.78 Lloyd et al 2012 Lloyd et al 2012 Brusatte et al 2014 Close et al 2015 Lloyd 2016 Wobble index:
- 73. Conclusions
- 74. Conclusions
- 75. Conclusions