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

1. Flexible Modeling of
Morphological Characters for
Phylogenetic Inference
April Wright
Will Pett
Tracy Heath
@wrightingapril

2. Challenges of Modeling
Morphological Data
Common meaning is not carried across characters

3. Challenges of Modeling
Morphological Data
Nucleotides do carry common meaning across
characters
ACTGAGTCGAATGCTGGGAGCTA

4. Challenges of Modeling
Morphological Data
Nucleotides do carry common meaning across
characters
A G
C T

5. Challenges of Modeling
Morphological Data
Common meaning is not carried across characters
01110112011131102210

6. Challenges of Modeling
Morphological Data
Common meaning is not carried across characters
01110112011131102210

7. Challenges of Modeling
Morphological Data
Common meaning is not carried across characters
01110112011131102210
0
0 1

8. Challenges of Modeling
Morphological Data
Common meaning is not carried across characters
01110112011131102210
0
0 1
0
0 1
1

9. Challenges of Modeling
Morphological Data
Image by Chris Smith

10. Challenges of Modeling
Morphological Data
Image by Chris Smith

11. Challenges of Modeling
Morphological Data
Image by Chris Smith

12. Challenges of Modeling
Morphological Data
0 1
Common meaning is not carried across characters
The Mk Model
(Lewis, 2001)

13. Challenges of Modeling
Morphological Data
0 1
2 3
Common meaning is not carried across characters
The Mk Model

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. 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. 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. 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. 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. 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. Ant Morphological Data
Image by Steve Shattuck
• Recoded characters from Barden
and Grimaldi 2016; Keller 2011
• 164 characters, 135 taxa

21. Ant Morphological Data
Image by Steve Shattuck
• Recoded characters from Barden
and Grimaldi 2016; Keller 2011
• 164 characters, 135 taxa
byfir001

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. Asymmetric Beta Prior
↵ 6=

24. Asymmetric Beta Prior
↵ 6=

25. Asymmetric Beta Prior
↵ 6=
0 1
1 0

26. Asymmetric Beta Prior
↵ 6=
0 1
1 0
0 1
1 0

27. Asymmetric Beta Prior
↵ 6=
0 1
1 0
0 1
1 0

28. Asymmetric Beta Prior
↵ 6=
0 1
1 0
0 1
1 0
0 1
1 0

29. Asymmetric Beta Prior
↵ 6=
0 1
1 0
0 1
1 0
0 1
1 0
0 1
1 0

30. Symmetric Beta Prior
↵ =
This is a special case of the asymmetrical Beta
Percentage of transitions
0 to 1
1 to 0

31. Asymmetric Beta Prior
We also implemented a multistate generalization
in which state frequencies are drawn from a Dirichlet
prior of k dimensions

32. Ant Morphological Data
• Recoded from Barden and
Grimaldi 2016; Keller 2011
• 164 characters, 135 taxa
Image by Steve Shattuck
byfir001

33. Ant Morphological Data
• Estimated phylogeny
from binary data sets
using discrete Beta
model
Image by Steve Shattuck
byfir001

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. Asymmetric Beta Prior
↵ 6=
0 1
1 0
0 1
1 0

36. Results: Asymmetric Beta
Model
• Does using the Asymmetric Beta Model improve
model fit for this dataset?

37. Asymmetric Beta Model
Improves Model Fit

38. Asymmetric Beta Model
Improves Model Fit
Mk model

39. Amount of Heterogeneity Is
Detectable With Model Fitting

40. State Frequencies Biased
Toward 0 Character

41. State Frequencies Biased
Toward 0 Character
More 0 1 transitions in dataset

42. Results: Asymmetric
Multistate Model
• Does using the asymmetric multistate model
improve model fit for this dataset?

43. Asymmetric Multistate Model
Improves Model Fit

44. Asymmetric Multistate Model
Improves Model Fit

45. Improved Models Improve
Phylogeny

46. Improved Models Improve
Phylogeny

47. Improved Models Improve
Phylogeny

48. Improved Models Improve
Phylogeny

49. Improved Models Improve
Phylogeny

50. Improved Models Improve
Phylogeny

51. Improved Models Improve
Phylogeny

52. Improved Models Improve
Phylogeny

53. Improved Models Improve
Phylogeny
PP > .9
PP > .5
PP > .1

54. Conclusions
• Allowing for transition rate asymmetry in both
binary and multistate characters is very helpful in
this dataset

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. 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. 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. Ant Phylogeny Remains
Challenging
“There are only so many ways to make an ant”
-Corrie Moreau

59. Wright Lab

60. Ant Phylogeny Is
Challenging
“There are only so many ways to make an ant”
-Corrie Moreau

61. What means for ants?

62. Results: Asymmetric Beta
Model

63. Results: Asymmetric Beta
Model