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Measuring morphological diversity and tempo using
discrete characters: advantages and disadvantages of
including additiona...
Acknowledgements
Emma SherrattThomas Guillerme
Discrete morphology
Discrete morphology
Discrete morphology
?
Discrete morphology
Discrete morphology
Discrete morphology
github.com/graemetlloyd/Claddis
Claddis
Lloyd 2016
github.com/graemetlloyd/Claddis
Claddis
Lloyd 2016
github.com/graemetlloyd/Claddis
Claddis
Lloyd 2016
github.com/graemetlloyd/Claddis
Claddis
Lloyd 2016
STR
github.com/graemetlloyd/Claddis
Claddis
Lloyd 2016
STR
#NEXUS
TNT/Hennig86
Claddis
Claddis
?
Claddis
(01)?
Claddis
(01)
0 1 2
1
1
?
Claddis
(01)
0 1 2
1
1
?
Outline
Phylogeny and disparity
Phylogeny and disparity
Increase sample size
Brusatte et al 2011
Phylogeny and disparity
Increase sample size Estimate missing
states
Brusatte et al 2011; Butler et al 2011
Phylogeny and disparity
Increase sample size Estimate missing
states
Brusatte et al 2011; Butler et al 2011; Hopkins and S...
Two phylomorphospace types
Two phylomorphospace types
Two phylomorphospace types
Brusatte et al 2011; Butler et al 2011
Two phylomorphospace types
Brusatte et al 2011; Butler et al 2011
Two phylomorphospace types
Brusatte et al 2011; Butler et al 2011; Hopkins and Smith 2015
Two phylomorphospace types
Two phylomorphospace types
Estimatetipstates
Estimate all ancestral states
N Y
NY
Two phylomorphospace types
Estimatetipstates
Estimate all ancestral states
N Y
NY
Two phylomorphospace types
Estimatetipstates
Estimate all ancestral states
N Y
NY
Questions
Questions
How do phylomorphospace choices affect our inferences?
To what degree are we measuring phylogenetic rather than
...
Questions
How do phylomorphospace choices affect our inferences?
To what degree are we measuring phylogenetic rather than
...
Disparity dataset
152 taxa | 853 characters
Disparity dataset
Results: layout
N Y
NY
N Y
NY
N Y
NY
N Y
NY
Results: scree plots
Lloyd in prep
Results: visualisation
Lloyd in prep
r = 0.188
r = 0.204
r = 0.354
r = 0.653
r = 0.396
r = 0.841
Results: phylogenetic correlation
Lloyd in prep
Results: root distance
Lloyd in prep
Results: root distance rate
Lloyd in prep
Rate equations
Rate equations
π‘…π‘Žπ‘‘π‘’ =
πΆβ„Žπ‘Žπ‘›π‘”π‘’
π‘‡π‘–π‘šπ‘’
Rate equations
π‘…π‘Žπ‘‘π‘’ =
πΆβ„Žπ‘Žπ‘›π‘”π‘’
π‘‡π‘–π‘šπ‘’
π‘…π‘Žπ‘‘π‘’ =
πΆβ„Žπ‘Žπ‘›π‘”π‘’
π‘‡π‘–π‘šπ‘’ Γ— πΆπ‘œπ‘šπ‘π‘™π‘’π‘‘π‘’π‘›π‘’π‘ π‘ 
Rate questions
Rate questions
Rate questions
Rate questions
Rate questions
Rate questions
Rate questions
Time
Rate questions
Time Change
Rate questions
Time Change
Completeness
Rate time series
Rate time series
Ruta et al 2006
Branches binned
(Time)
Rate time series
Ruta et al 2006; Lloyd et al 2012
Stochastic changes
(Change)
Branches binned
(Time)
Rate time series
Ruta et al 2006; Lloyd et al 2012; Close et al 2015
Stochastic changes
(Change)
Branches binned
(Time)
We...
Questions
Questions
How does ASR choice affect rate time series?
How does correcting for completeness affect rate time series?
Questions
How does ASR choice affect rate time series?
How does correcting for completeness affect rate time series?
Rate dataset
86 taxa | 91 characters
Rate dataset
Westoll 1949
Rate results
Rate results
ACCTRAN DELTRAN Likelihood Likelihood
+ Corr. 1
Likelihood
+ Corr. 2
Rate results
ACCTRAN DELTRAN Likelihood Likelihood
+ Corr. 1
Likelihood
+ Corr. 2
Lloyd
et al
2012
Lloyd
et al
2012
Brusat...
Rate results
ACCTRAN DELTRAN Likelihood Likelihood
+ Corr. 1
Likelihood
+ Corr. 2
Lloyd
et al
2012
Lloyd
et al
2012
Brusat...
Rate results
ACCTRAN DELTRAN Likelihood Likelihood
+ Corr. 1
Likelihood
+ Corr. 2
Lloyd
et al
2012
Lloyd
et al
2012
Brusat...
Rate results
ACCTRAN DELTRAN Likelihood Likelihood
+ Corr. 1
Likelihood
+ Corr. 2
1.39 1.77 0.78 0.23 0.78
Lloyd
et al
201...
Conclusions
Conclusions
Conclusions
Conclusions
1.77
0.78
Conclusions
1.77
0.78
Measuring morphological diversity and tempo using discrete characters: advantages and disadvantages of including additiona...
Measuring morphological diversity and tempo using discrete characters: advantages and disadvantages of including additiona...
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Measuring morphological diversity and tempo using discrete characters: advantages and disadvantages of including additional phylogenetic information

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Measuring morphological diversity and tempo using discrete characters: advantages and disadvantages of including additional phylogenetic information

  1. 1. Measuring morphological diversity and tempo using discrete characters: advantages and disadvantages of including additional phylogenetic information Graeme T. Lloyd @GraemeTLloyd
  2. 2. Acknowledgements Emma SherrattThomas Guillerme
  3. 3. Discrete morphology
  4. 4. Discrete morphology
  5. 5. Discrete morphology ?
  6. 6. Discrete morphology
  7. 7. Discrete morphology
  8. 8. Discrete morphology
  9. 9. github.com/graemetlloyd/Claddis Claddis Lloyd 2016
  10. 10. github.com/graemetlloyd/Claddis Claddis Lloyd 2016
  11. 11. github.com/graemetlloyd/Claddis Claddis Lloyd 2016
  12. 12. github.com/graemetlloyd/Claddis Claddis Lloyd 2016 STR
  13. 13. github.com/graemetlloyd/Claddis Claddis Lloyd 2016 STR #NEXUS TNT/Hennig86
  14. 14. Claddis
  15. 15. Claddis ?
  16. 16. Claddis (01)?
  17. 17. Claddis (01) 0 1 2 1 1 ?
  18. 18. Claddis (01) 0 1 2 1 1 ?
  19. 19. Outline
  20. 20. Phylogeny and disparity
  21. 21. Phylogeny and disparity Increase sample size Brusatte et al 2011
  22. 22. Phylogeny and disparity Increase sample size Estimate missing states Brusatte et al 2011; Butler et al 2011
  23. 23. Phylogeny and disparity Increase sample size Estimate missing states Brusatte et al 2011; Butler et al 2011; Hopkins and Smith 2015 Create phylomorphospace
  24. 24. Two phylomorphospace types
  25. 25. Two phylomorphospace types
  26. 26. Two phylomorphospace types Brusatte et al 2011; Butler et al 2011
  27. 27. Two phylomorphospace types Brusatte et al 2011; Butler et al 2011
  28. 28. Two phylomorphospace types Brusatte et al 2011; Butler et al 2011; Hopkins and Smith 2015
  29. 29. Two phylomorphospace types
  30. 30. Two phylomorphospace types Estimatetipstates Estimate all ancestral states N Y NY
  31. 31. Two phylomorphospace types Estimatetipstates Estimate all ancestral states N Y NY
  32. 32. Two phylomorphospace types Estimatetipstates Estimate all ancestral states N Y NY
  33. 33. Questions
  34. 34. Questions How do phylomorphospace choices affect our inferences? To what degree are we measuring phylogenetic rather than morphological signal?
  35. 35. Questions How do phylomorphospace choices affect our inferences? To what degree are we measuring phylogenetic rather than morphological signal?
  36. 36. Disparity dataset 152 taxa | 853 characters
  37. 37. Disparity dataset
  38. 38. Results: layout N Y NY N Y NY N Y NY N Y NY
  39. 39. Results: scree plots Lloyd in prep
  40. 40. Results: visualisation Lloyd in prep
  41. 41. r = 0.188 r = 0.204 r = 0.354 r = 0.653 r = 0.396 r = 0.841 Results: phylogenetic correlation Lloyd in prep
  42. 42. Results: root distance Lloyd in prep
  43. 43. Results: root distance rate Lloyd in prep
  44. 44. Rate equations
  45. 45. Rate equations π‘…π‘Žπ‘‘π‘’ = πΆβ„Žπ‘Žπ‘›π‘”π‘’ π‘‡π‘–π‘šπ‘’
  46. 46. Rate equations π‘…π‘Žπ‘‘π‘’ = πΆβ„Žπ‘Žπ‘›π‘”π‘’ π‘‡π‘–π‘šπ‘’ π‘…π‘Žπ‘‘π‘’ = πΆβ„Žπ‘Žπ‘›π‘”π‘’ π‘‡π‘–π‘šπ‘’ Γ— πΆπ‘œπ‘šπ‘π‘™π‘’π‘‘π‘’π‘›π‘’π‘ π‘ 
  47. 47. Rate questions
  48. 48. Rate questions
  49. 49. Rate questions
  50. 50. Rate questions
  51. 51. Rate questions
  52. 52. Rate questions
  53. 53. Rate questions Time
  54. 54. Rate questions Time Change
  55. 55. Rate questions Time Change Completeness
  56. 56. Rate time series
  57. 57. Rate time series Ruta et al 2006 Branches binned (Time)
  58. 58. Rate time series Ruta et al 2006; Lloyd et al 2012 Stochastic changes (Change) Branches binned (Time)
  59. 59. Rate time series Ruta et al 2006; Lloyd et al 2012; Close et al 2015 Stochastic changes (Change) Branches binned (Time) Weighted average (Completeness)
  60. 60. Questions
  61. 61. Questions How does ASR choice affect rate time series? How does correcting for completeness affect rate time series?
  62. 62. Questions How does ASR choice affect rate time series? How does correcting for completeness affect rate time series?
  63. 63. Rate dataset 86 taxa | 91 characters
  64. 64. Rate dataset Westoll 1949
  65. 65. Rate results
  66. 66. Rate results ACCTRAN DELTRAN Likelihood Likelihood + Corr. 1 Likelihood + Corr. 2
  67. 67. 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
  68. 68. 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
  69. 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. 70. 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:
  71. 71. Conclusions
  72. 72. Conclusions
  73. 73. Conclusions
  74. 74. Conclusions 1.77 0.78
  75. 75. Conclusions 1.77 0.78

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