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Flexible Modeling of
Morphological Characters for
Phylogenetic Inference
April Wright
Will Pett
Tracy Heath
@wrightingapril
Challenges of Modeling
Morphological Data
Common meaning is not carried across characters
Challenges of Modeling
Morphological Data
Nucleotides do carry common meaning across
characters
ACTGAGTCGAATGCTGGGAGCTA
Challenges of Modeling
Morphological Data
Nucleotides do carry common meaning across
characters
A G
C T
Challenges of Modeling
Morphological Data
Common meaning is not carried across characters
01110112011131102210
Challenges of Modeling
Morphological Data
Common meaning is not carried across characters
01110112011131102210
Challenges of Modeling
Morphological Data
Common meaning is not carried across characters
01110112011131102210
0
0 1
Challenges of Modeling
Morphological Data
Common meaning is not carried across characters
01110112011131102210
0
0 1
0
0 1...
Challenges of Modeling
Morphological Data
Image by Chris Smith
Challenges of Modeling
Morphological Data
Image by Chris Smith
Challenges of Modeling
Morphological Data
Image by Chris Smith
Challenges of Modeling
Morphological Data
0 1
Common meaning is not carried across characters
The Mk Model
(Lewis, 2001)
Challenges of Modeling
Morphological Data
0 1
2 3
Common meaning is not carried across characters
The Mk Model
Symmetric Beta Prior
↵ =
Figure from Wright et al. 2016,
model implemented in MrBayes,
Ronquist and Huelsenbeck 2003
Perce...
Symmetric Beta Prior
↵ =
Figure from Wright et al. 2016,
model implemented in MrBayes,
Ronquist and Huelsenbeck 2003
Perce...
Ant Morphological Data
Image by Steve Shattuck
Ants have a rich fossil record, including many stem lineages,
as well as ma...
Ant Morphological Data
Image by Steve Shattuck
Presence of wasplike
features that
are lost after
divergence of
Sphecomyrmi...
Ant Morphological Data
Image by Steve Shattuck
Presence of wasplike
features that
are lost after
divergence of
Sphecomyrmi...
Ant Morphological Data
Image by Steve Shattuck
Presence of wasplike
features that
are lost after
divergence of
Sphecomyrmi...
Ant Morphological Data
Image by Steve Shattuck
• Recoded characters from Barden
and Grimaldi 2016; Keller 2011
• 164 chara...
Ant Morphological Data
Image by Steve Shattuck
• Recoded characters from Barden
and Grimaldi 2016; Keller 2011
• 164 chara...
Symmetric Beta Prior
↵ =
Figure from Wright et al. 2016,
model implemented in MrBayes,
Ronquist and Huelsenbeck 2003
Perce...
Asymmetric Beta Prior
↵ 6=
Asymmetric Beta Prior
↵ 6=
Asymmetric Beta Prior
↵ 6=
0 1
1 0
Asymmetric Beta Prior
↵ 6=
0 1
1 0
0 1
1 0
Asymmetric Beta Prior
↵ 6=
0 1
1 0
0 1
1 0
Asymmetric Beta Prior
↵ 6=
0 1
1 0
0 1
1 0
0 1
1 0
Asymmetric Beta Prior
↵ 6=
0 1
1 0
0 1
1 0
0 1
1 0
0 1
1 0
Symmetric Beta Prior
↵ =
This is a special case of the asymmetrical Beta
Percentage of transitions
0 to 1
1 to 0
Asymmetric Beta Prior
We also implemented a multistate generalization
in which state frequencies are drawn from a Dirichle...
Ant Morphological Data
• Recoded from Barden and
Grimaldi 2016; Keller 2011
• 164 characters, 135 taxa
Image by Steve Shat...
Ant Morphological Data
• Estimated phylogeny
from binary data sets
using discrete Beta
model
Image by Steve Shattuck
byfir0...
Ant Morphological Data
• Estimated phylogeny
from binary data sets
using discrete Beta
model
• Phylogeny using
binary + mu...
Asymmetric Beta Prior
↵ 6=
0 1
1 0
0 1
1 0
Results: Asymmetric Beta
Model
• Does using the Asymmetric Beta Model improve
model fit for this dataset?
Asymmetric Beta Model
Improves Model Fit
Asymmetric Beta Model
Improves Model Fit
Mk model
Amount of Heterogeneity Is
Detectable With Model Fitting
State Frequencies Biased
Toward 0 Character
State Frequencies Biased
Toward 0 Character
More 0 1 transitions in dataset
Results: Asymmetric
Multistate Model
• Does using the asymmetric multistate model
improve model fit for this dataset?
Asymmetric Multistate Model
Improves Model Fit
Asymmetric Multistate Model
Improves Model Fit
Improved Models Improve
Phylogeny
Improved Models Improve
Phylogeny
Improved Models Improve
Phylogeny
Improved Models Improve
Phylogeny
Improved Models Improve
Phylogeny
Improved Models Improve
Phylogeny
Improved Models Improve
Phylogeny
Improved Models Improve
Phylogeny
Improved Models Improve
Phylogeny
PP > .9
PP > .5
PP > .1
Conclusions
• Allowing for transition rate asymmetry in both
binary and multistate characters is very helpful in
this data...
Conclusions
• Allowing for transition rate asymmetry in both
binary and multistate characters is very helpful in
this data...
Conclusions
• Allowing for transition rate asymmetry in both
binary and multistate characters is very helpful in
this data...
Thank You
The Heath Lab
Tracy Heath
Walker Pett
Jordan Satler
Kevin Quinteros
Wade Dismukes
Roberta Graboski Mendes
Andre ...
Ant Phylogeny Remains
Challenging
“There are only so many ways to make an ant”
-Corrie Moreau
Wright Lab
Ant Phylogeny Is
Challenging
“There are only so many ways to make an ant”
-Corrie Moreau
What means for ants?
Results: Asymmetric Beta
Model
Results: Asymmetric Beta
Model
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Evol2017

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Published on

Talk for evolution 2017
Tutorial at: http://revbayes.github.io/tutorials.html "Models of morphological character evolution (substitution models)."

Published in: Science
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Evol2017

  1. 1. Flexible Modeling of Morphological Characters for Phylogenetic Inference April Wright Will Pett Tracy Heath @wrightingapril
  2. 2. Challenges of Modeling Morphological Data Common meaning is not carried across characters
  3. 3. Challenges of Modeling Morphological Data Nucleotides do carry common meaning across characters ACTGAGTCGAATGCTGGGAGCTA
  4. 4. Challenges of Modeling Morphological Data Nucleotides do carry common meaning across characters A G C T
  5. 5. Challenges of Modeling Morphological Data Common meaning is not carried across characters 01110112011131102210
  6. 6. Challenges of Modeling Morphological Data Common meaning is not carried across characters 01110112011131102210
  7. 7. Challenges of Modeling Morphological Data Common meaning is not carried across characters 01110112011131102210 0 0 1
  8. 8. Challenges of Modeling Morphological Data Common meaning is not carried across characters 01110112011131102210 0 0 1 0 0 1 1
  9. 9. Challenges of Modeling Morphological Data Image by Chris Smith
  10. 10. Challenges of Modeling Morphological Data Image by Chris Smith
  11. 11. Challenges of Modeling Morphological Data Image by Chris Smith
  12. 12. Challenges of Modeling Morphological Data 0 1 Common meaning is not carried across characters The Mk Model (Lewis, 2001)
  13. 13. Challenges of Modeling Morphological Data 0 1 2 3 Common meaning is not carried across characters The Mk Model
  14. 14. Symmetric Beta Prior ↵ = Figure from Wright et al. 2016, model implemented in MrBayes, Ronquist and Huelsenbeck 2003 Percentage of transitions 0 to 1 1 to 0
  15. 15. Symmetric Beta Prior ↵ = Figure from Wright et al. 2016, model implemented in MrBayes, Ronquist and Huelsenbeck 2003 Percentage of transitions 0 to 1 1 to 0
  16. 16. Ant Morphological Data Image by Steve Shattuck Ants have a rich fossil record, including many stem lineages, as well as many scored specimens from extant lineages
  17. 17. Ant Morphological Data Image by Steve Shattuck Presence of wasplike features that are lost after divergence of Sphecomyrminae from the rest of the ants 1 0
  18. 18. Ant Morphological Data Image by Steve Shattuck Presence of wasplike features that are lost after divergence of Sphecomyrminae from the rest of the ants 1 0 Presence of ant apomorphies 0 1
  19. 19. Ant Morphological Data Image by Steve Shattuck Presence of wasplike features that are lost after divergence of Sphecomyrminae from the rest of the ants 1 0 Presence of ant apomorphies 0 1 Strong violation of equal transition rates model
  20. 20. Ant Morphological Data Image by Steve Shattuck • Recoded characters from Barden and Grimaldi 2016; Keller 2011 • 164 characters, 135 taxa
  21. 21. Ant Morphological Data Image by Steve Shattuck • Recoded characters from Barden and Grimaldi 2016; Keller 2011 • 164 characters, 135 taxa byfir001
  22. 22. Symmetric Beta Prior ↵ = Figure from Wright et al. 2016, model implemented in MrBayes, Ronquist and Huelsenbeck 2003 Percentage of transitions 0 to 1 1 to 0
  23. 23. Asymmetric Beta Prior ↵ 6=
  24. 24. Asymmetric Beta Prior ↵ 6=
  25. 25. Asymmetric Beta Prior ↵ 6= 0 1 1 0
  26. 26. Asymmetric Beta Prior ↵ 6= 0 1 1 0 0 1 1 0
  27. 27. Asymmetric Beta Prior ↵ 6= 0 1 1 0 0 1 1 0
  28. 28. Asymmetric Beta Prior ↵ 6= 0 1 1 0 0 1 1 0 0 1 1 0
  29. 29. Asymmetric Beta Prior ↵ 6= 0 1 1 0 0 1 1 0 0 1 1 0 0 1 1 0
  30. 30. Symmetric Beta Prior ↵ = This is a special case of the asymmetrical Beta Percentage of transitions 0 to 1 1 to 0
  31. 31. Asymmetric Beta Prior We also implemented a multistate generalization in which state frequencies are drawn from a Dirichlet prior of k dimensions
  32. 32. Ant Morphological Data • Recoded from Barden and Grimaldi 2016; Keller 2011 • 164 characters, 135 taxa Image by Steve Shattuck byfir001
  33. 33. Ant Morphological Data • Estimated phylogeny from binary data sets using discrete Beta model Image by Steve Shattuck byfir001
  34. 34. Ant Morphological Data • Estimated phylogeny from binary data sets using discrete Beta model • Phylogeny using binary + multistate data with generalized Beta model Image by Steve Shattuck byfir001
  35. 35. Asymmetric Beta Prior ↵ 6= 0 1 1 0 0 1 1 0
  36. 36. Results: Asymmetric Beta Model • Does using the Asymmetric Beta Model improve model fit for this dataset?
  37. 37. Asymmetric Beta Model Improves Model Fit
  38. 38. Asymmetric Beta Model Improves Model Fit Mk model
  39. 39. Amount of Heterogeneity Is Detectable With Model Fitting
  40. 40. State Frequencies Biased Toward 0 Character
  41. 41. State Frequencies Biased Toward 0 Character More 0 1 transitions in dataset
  42. 42. Results: Asymmetric Multistate Model • Does using the asymmetric multistate model improve model fit for this dataset?
  43. 43. Asymmetric Multistate Model Improves Model Fit
  44. 44. Asymmetric Multistate Model Improves Model Fit
  45. 45. Improved Models Improve Phylogeny
  46. 46. Improved Models Improve Phylogeny
  47. 47. Improved Models Improve Phylogeny
  48. 48. Improved Models Improve Phylogeny
  49. 49. Improved Models Improve Phylogeny
  50. 50. Improved Models Improve Phylogeny
  51. 51. Improved Models Improve Phylogeny
  52. 52. Improved Models Improve Phylogeny
  53. 53. Improved Models Improve Phylogeny PP > .9 PP > .5 PP > .1
  54. 54. Conclusions • Allowing for transition rate asymmetry in both binary and multistate characters is very helpful in this dataset
  55. 55. Conclusions • Allowing for transition rate asymmetry in both binary and multistate characters is very helpful in this dataset • The number of transition symmetry categories is detectable with Bayes factor model fitting
  56. 56. Conclusions • Allowing for transition rate asymmetry in both binary and multistate characters is very helpful in this dataset • The number of transition symmetry categories is detectable with Bayes factor model fitting • Resolving ant phylogenetic relationships remains challenging, but hopeful
  57. 57. Thank You The Heath Lab Tracy Heath Walker Pett Jordan Satler Kevin Quinteros Wade Dismukes Roberta Graboski Mendes Andre Flores Patrick Mendoza Helpful Discussions Corrie Moreau Paul Lewis Benjamin Blanchard Philip Barden Mark Holder DEB-1556615, DEB-1256993 DBI-1612858 revbayes.github.io
  58. 58. Ant Phylogeny Remains Challenging “There are only so many ways to make an ant” -Corrie Moreau
  59. 59. Wright Lab
  60. 60. Ant Phylogeny Is Challenging “There are only so many ways to make an ant” -Corrie Moreau
  61. 61. What means for ants?
  62. 62. Results: Asymmetric Beta Model
  63. 63. Results: Asymmetric Beta Model

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