PDU2 presentation

1. A novel metatree approach to generating large
phylogenetic hypotheses of extinct taxa
Graeme T. Lloyd @GraemeTLloyd

2. Acknowledgements
Katie Davis

3. Where evolution happens

4. Where evolution happens

5. Phylogeny and macroevolution

6. Phylogeny and macroevolution

7. Phylogeny and macroevolution

8. Phylogeny and macroevolution

9. Phylogeny and macroevolution
vs

10. Go big or go home

11. 1200 spp
Go big or go home

12. 1200 spp
Go big or go home
2000 spp

13. 1200 spp
Go big or go home
2000 spp
5000 spp

14. 1200 spp
Go big or go home
20000 spp
2000 spp
5000 spp

15. Largest morphological matrices

16. Largest morphological matrices
86 | 4541188 | 2954192 | 610
Gauthier et al 2012; Livezey and Zusi 2007; O’Leary et al 2013

17. A practical alternative

18. A practical alternative

19. Pipelines

20. Pipelines
Informal supertree:

21. Pipelines
Formal supertree:
Informal supertree:

22. Pipelines
Informal supertree:
Formal supertree:
Metatree:

23. Problems with entering trees

24. Problems with entering trees
Supertree
Published figure:
Metatree
Tree from reanalysed matrix:
Xu et al 2013

25. Problems with entering trees
Bell and Lloyd 2015

26. Problems with entering trees
Bell and Lloyd 2015

27. Metatree pipeline

28. Metatree pipeline
Data
collection
Taxonomic
reconciliation
Filter
data
Add
“taxonotree”
Inference
Safe Taxon
Reduction
Weighting
scheme

29. Metatree pipeline
Data
collection
Taxonomic
reconciliation
Filter
data
Add
“taxonotree”
Inference
Safe Taxon
Reduction
Weighting
scheme

30. Metatree pipeline
Data
collection

31. Metatree pipeline
graemetlloyd.com
Data
collection

32. Metatree pipeline
graemetlloyd.com
Data
collection
2359 datasets

33. Metatree pipeline
graemetlloyd.com
Data
collection
2359 datasets

34. Metatree pipeline
graemetlloyd.com
Data
collection
2359 datasets

35. Metatree pipeline
Data
collection
A B C D E
Baum 1992; Ragan 1992
A
B
C
D
E
Matrix
Representation

36. Metatree pipeline
Data
collection
Matrix
Representation
A B C D E
A
B
C
D
E
0
1
1
0
0
Baum 1992; Ragan 1992

37. Metatree pipeline
Data
collection
Matrix
Representation
A B C D E
A
B
C
D
E
0
1
1
0
0
0
0
0
1
1
Baum 1992; Ragan 1992

38. Metatree pipeline
Data
collection
Matrix
Representation
A B C D E
A
B
C
D
E
0
1
1
0
0
0
0
0
1
1
0
1
1
1
1
Baum 1992; Ragan 1992

39. Metatree pipeline
Data
collection
A B C D E
A
B
C
D
E
0
1
1
0
0
0
0
0
1
1
0
1
1
1
1
Baum 1992; Ragan 1992

40. Metatree pipeline
Data
collection
Matrix
Representation ?

41. Metatree pipeline
Taxonomic
reconciliation

42. Metatree pipeline
Taxonomic
reconciliation
Outgroup
Shortened name
Junior synonym
Valid taxon
Invalid taxon
Higher taxon
Prune
Full name
Senior synonym
Nothing
Prune
Constituent species

43. Metatree pipeline
Taxonomic
reconciliation

44. Metatree pipeline
Taxonomic
reconciliation

45. Metatree pipeline
Taxonomic
reconciliation 13285 962

46. Metatree pipeline
Filter
data

47. Metatree pipeline
Filter
data

48. Metatree pipeline
1998
Filter
data

49. Metatree pipeline
Add
“taxonotree”

50. Metatree pipeline
A
B
C
D
E
F
G
H
I
J
K
L
Class Order Family Genus
Add
“taxonotree”

51. Metatree pipeline
Weighting
scheme

52. Metatree pipeline
Weighting
scheme

53. Metatree pipeline
Safe Taxon
Reduction

54. Metatree pipeline
github.com/graemetlloyd/Claddis
Safe Taxon
Reduction

55. Metatree pipeline
github.com/graemetlloyd/Claddis
Safe Taxon
Reduction -50 OTUs

56. Metatree pipeline
Inference

57. Metatree pipeline
Inference

58. Other metatrees

59. Other metatrees
Lloyd et al 2008; Lloyd 2014; Clarke et al in revision

60. Conclusions

61. Conclusions

62. Conclusions

63. Conclusions

64. Conclusions