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A novel metatree approach to generating large
phylogenetic hypotheses of extinct taxa
Graeme T. Lloyd @GraemeTLloyd
Acknowledgements
Katie Davis
Where evolution happens
Where evolution happens
Phylogeny and macroevolution
Phylogeny and macroevolution
Phylogeny and macroevolution
Phylogeny and macroevolution
Phylogeny and macroevolution
vs
Go big or go home
1200 spp
Go big or go home
1200 spp
Go big or go home
2000 spp
1200 spp
Go big or go home
2000 spp
5000 spp
1200 spp
Go big or go home
20000 spp
2000 spp
5000 spp
Largest morphological matrices
Largest morphological matrices
86 | 4541188 | 2954192 | 610
Gauthier et al 2012; Livezey and Zusi 2007; O’Leary et al 2013
A practical alternative
A practical alternative
Pipelines
Pipelines
Informal supertree:
Pipelines
Formal supertree:
Informal supertree:
Pipelines
Informal supertree:
Formal supertree:
Metatree:
Problems with entering trees
Problems with entering trees
Supertree
Published figure:
Metatree
Tree from reanalysed matrix:
Xu et al 2013
Problems with entering trees
Bell and Lloyd 2015
Problems with entering trees
Bell and Lloyd 2015
Metatree pipeline
Metatree pipeline
Data
collection
Taxonomic
reconciliation
Filter
data
Add
“taxonotree”
Inference
Safe Taxon
Reduction
Wei...
Metatree pipeline
Data
collection
Taxonomic
reconciliation
Filter
data
Add
“taxonotree”
Inference
Safe Taxon
Reduction
Wei...
Metatree pipeline
Data
collection
Metatree pipeline
graemetlloyd.com
Data
collection
Metatree pipeline
graemetlloyd.com
Data
collection
2359 datasets
Metatree pipeline
graemetlloyd.com
Data
collection
2359 datasets
Metatree pipeline
graemetlloyd.com
Data
collection
2359 datasets
Metatree pipeline
Data
collection
A B C D E
Baum 1992; Ragan 1992
A
B
C
D
E
Matrix
Representation
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
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
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...
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
Metatree pipeline
Data
collection
Matrix
Representation ?
Metatree pipeline
Taxonomic
reconciliation
Metatree pipeline
Taxonomic
reconciliation
Outgroup
Shortened name
Junior synonym
Valid taxon
Invalid taxon
Higher taxon
P...
Metatree pipeline
Taxonomic
reconciliation
Metatree pipeline
Taxonomic
reconciliation
Metatree pipeline
Taxonomic
reconciliation 13285 962
Metatree pipeline
Filter
data
Metatree pipeline
Filter
data
Metatree pipeline
1998
Filter
data
Metatree pipeline
Add
“taxonotree”
Metatree pipeline
A
B
C
D
E
F
G
H
I
J
K
L
Class Order Family Genus
Add
“taxonotree”
Metatree pipeline
Weighting
scheme
Metatree pipeline
Weighting
scheme
Metatree pipeline
Safe Taxon
Reduction
Metatree pipeline
github.com/graemetlloyd/Claddis
Safe Taxon
Reduction
Metatree pipeline
github.com/graemetlloyd/Claddis
Safe Taxon
Reduction -50 OTUs
Metatree pipeline
Inference
Metatree pipeline
Inference
Other metatrees
Other metatrees
Lloyd et al 2008; Lloyd 2014; Clarke et al in revision
Conclusions
Conclusions
Conclusions
Conclusions
Conclusions
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A novel metatree approach to generating large phylogenetic hypotheses of extinct taxa

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A novel metatree approach to generating large phylogenetic hypotheses of extinct taxa

  1. 1. A novel metatree approach to generating large phylogenetic hypotheses of extinct taxa Graeme T. Lloyd @GraemeTLloyd
  2. 2. Acknowledgements Katie Davis
  3. 3. Where evolution happens
  4. 4. Where evolution happens
  5. 5. Phylogeny and macroevolution
  6. 6. Phylogeny and macroevolution
  7. 7. Phylogeny and macroevolution
  8. 8. Phylogeny and macroevolution
  9. 9. Phylogeny and macroevolution vs
  10. 10. Go big or go home
  11. 11. 1200 spp Go big or go home
  12. 12. 1200 spp Go big or go home 2000 spp
  13. 13. 1200 spp Go big or go home 2000 spp 5000 spp
  14. 14. 1200 spp Go big or go home 20000 spp 2000 spp 5000 spp
  15. 15. Largest morphological matrices
  16. 16. Largest morphological matrices 86 | 4541188 | 2954192 | 610 Gauthier et al 2012; Livezey and Zusi 2007; O’Leary et al 2013
  17. 17. A practical alternative
  18. 18. A practical alternative
  19. 19. Pipelines
  20. 20. Pipelines Informal supertree:
  21. 21. Pipelines Formal supertree: Informal supertree:
  22. 22. Pipelines Informal supertree: Formal supertree: Metatree:
  23. 23. Problems with entering trees
  24. 24. Problems with entering trees Supertree Published figure: Metatree Tree from reanalysed matrix: Xu et al 2013
  25. 25. Problems with entering trees Bell and Lloyd 2015
  26. 26. Problems with entering trees Bell and Lloyd 2015
  27. 27. Metatree pipeline
  28. 28. Metatree pipeline Data collection Taxonomic reconciliation Filter data Add “taxonotree” Inference Safe Taxon Reduction Weighting scheme
  29. 29. Metatree pipeline Data collection Taxonomic reconciliation Filter data Add “taxonotree” Inference Safe Taxon Reduction Weighting scheme
  30. 30. Metatree pipeline Data collection
  31. 31. Metatree pipeline graemetlloyd.com Data collection
  32. 32. Metatree pipeline graemetlloyd.com Data collection 2359 datasets
  33. 33. Metatree pipeline graemetlloyd.com Data collection 2359 datasets
  34. 34. Metatree pipeline graemetlloyd.com Data collection 2359 datasets
  35. 35. Metatree pipeline Data collection A B C D E Baum 1992; Ragan 1992 A B C D E Matrix Representation
  36. 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. 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. 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. 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. 40. Metatree pipeline Data collection Matrix Representation ?
  41. 41. Metatree pipeline Taxonomic reconciliation
  42. 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. 43. Metatree pipeline Taxonomic reconciliation
  44. 44. Metatree pipeline Taxonomic reconciliation
  45. 45. Metatree pipeline Taxonomic reconciliation 13285 962
  46. 46. Metatree pipeline Filter data
  47. 47. Metatree pipeline Filter data
  48. 48. Metatree pipeline 1998 Filter data
  49. 49. Metatree pipeline Add “taxonotree”
  50. 50. Metatree pipeline A B C D E F G H I J K L Class Order Family Genus Add “taxonotree”
  51. 51. Metatree pipeline Weighting scheme
  52. 52. Metatree pipeline Weighting scheme
  53. 53. Metatree pipeline Safe Taxon Reduction
  54. 54. Metatree pipeline github.com/graemetlloyd/Claddis Safe Taxon Reduction
  55. 55. Metatree pipeline github.com/graemetlloyd/Claddis Safe Taxon Reduction -50 OTUs
  56. 56. Metatree pipeline Inference
  57. 57. Metatree pipeline Inference
  58. 58. Other metatrees
  59. 59. Other metatrees Lloyd et al 2008; Lloyd 2014; Clarke et al in revision
  60. 60. Conclusions
  61. 61. Conclusions
  62. 62. Conclusions
  63. 63. Conclusions
  64. 64. Conclusions

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