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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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