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Curriculum vitae
• Fieldwork
• Labwork:
The world evolutionary radiation of the
cosmopolitan genus Myotis : biogeographic ...
Phyllostomidae and the
evolution of diet
Phylogeny & evolution of bats:
evolution of diet
Presented by : Yann Gager
Superv...
Phyllostomidae
Phyllostomidae and the evolution of diet
Phyllostomidae
• Leaf-nosed bats from the New World
Phyllostomidae
• Leaf-nosed bats from the New World
• ~ 160 species described (55 genus) :
More than 10% of Bats =
2nd Ord...
Phyllostomidae
• Leaf-nosed bats from the New World
• ~ 160 species described (55 genus) :
More than 10% of Bats =
2nd Ord...
Phyllostomidae
Blood
Phyllostomidae
Blood Plants
Phyllostomidae
Blood Plants Arthropods
Phyllostomidae
Blood Plants Arthropods Vertebrates
Goals of the study
Phyllostomidae and the evolution of diet
Goals of the study
• Reliable phylogenetic tree:
important sampling of species
and molecular data
Goals of the study
• Reliable phylogenetic tree:
important sampling of species
and molecular data
• Preliminary to the stu...
Samplings
Phyllostomidae and the evolution of diet
Samplings
• 120 species + 3 outgroups
Samplings
• 120 species + 3 outgroups
• Compilation & concatenation of genes* :
Supermatrix of 6883 aligned nucleotides
*(...
Samplings
• 120 species + 3 outgroups
• Compilation & concatenation of genes* :
Supermatrix of 6883 aligned nucleotides
12...
Phylogenetic analyses
Phyllostomidae and the evolution of diet
Phylogenetic analyses
• Maximum likelihood (GTR + Γ + INV)
Phylogenetic analyses
• Maximum likelihood (GTR + Γ + INV)
P ,MP ,M
Phylogenetic analyses
• Maximum likelihood (GTR + Γ + INV)
• Node support : Bootstrap (100 replicates)
Phylogenetic analyses
• Maximum likelihood (GTR + Γ + INV)
• Node support : Bootstrap (100 replicates)
• Inference of diet...
Evolution of diet
Phyllostomidae and the evolution of diet
Evolution of diet
• Function ACE with APE (R) :
Ancestral Character Estimation
Species 1
Species 2
?
Species 3
?
Evolution of diet
• Function ACE with APE (R) :
Ancestral Character Estimation
• Probabilistic model of estimation of the
...
Evolution of diet
• Function ACE with APE (R) :
Ancestral Character Estimation
• Probabilistic model of estimation of the
...
Evolution of diet
• Function ACE with APE (R) :
Ancestral Character Estimation
• Probabilistic model of estimation of the
...
Evolution of diet
• Function ACE with APE (R) :
Ancestral Character Estimation
• Probabilistic model of estimation of the
...
Phytophagy
Animalivory
Omnivory
Phytophagy
Animalivory
Omnivory
Phytophagy
Animalivory
Omnivory
Phytophagy
Animalivory
Omnivory
Phytophagy
Animalivory
Omnivory
Evolution of diet
• Specialisations, but opportunistic omnivory
– Food completion
Evolution of diet
• Specialisations, but opportunistic omnivory
– Food completion
– Survival when the favorite food is rare
Prospects
Phyllostomidae and the evolution of diet
Prospects
• To obtain a fully resolved phylogeny !
Prospects
• To obtain a fully resolved phylogeny !
1) More taxa
Prospects
• To obtain a fully resolved phylogeny !
1) More taxa
2) More genes
Prospects
• To obtain a fully resolved phylogeny !
1) More taxa
2) More genes
3) Both !
Prospects
• Well supported phylogenies:
Working basis for numerous research on bats!
Prospects
• Well supported phylogenies:
Working basis for numerous research on bats!
Life-history
traits
Artibeus sp.
Prospects
• Well supported phylogenies:
Working basis for numerous research on bats!
Systematics
Cistugo sp.
Prospects
• Well supported phylogenies:
Working basis for numerous research on bats!
Biogeography
Myotis spp.
Prospects
• Well supported phylogenies:
Working basis for numerous research on bats!
Conservation
Craseonycteris thonglong...
Acknowledgments
• Team Molecular phylogeny and Evolution:
E. Douzery, F. Botero, M. Ballenghien, P.
Gayral, C. Delsol
• Fu...
Thank you !
Supermatrix
• Drawbacks: Missing data
e.g. artefacts
• Benefits: Contribution for a phylogenetic
signalsignal
e.g ½ of 7kb...
Supermatrix
100
75
47
97
100
99
100
100
100
100
100
100
86
46
29
73
85
7395
67
85
97
General Time Reversible ( GTR )
A C G T
A - a∏C b∏G c∏T
C a∏A - d∏G e∏T
• Base frequencies ∏, substitution rates (from a
t...
• Nucleotide model of evolution
• General Time Reversible (GTR) with a gamma
distribution of rate variation (Γ) and a
prop...
Evolution of diet
• Matrix of rates of change of trophic level state
Phytophagy Omnivory Animalivory
Phytophagy NA 2,50 0
...
Rate change of trophic level
• ER = Equal rates
• SR = Synonym rates
Phytophagy Omnivory Animalivory
Phytophagy NA R1 R1
O...
Order
Chiroptera
Jones and Teeling, 2006
Chiroptera
Phyllostomidae
Blood
Phyllostomidae
Blood Plants
Phyllostomidae
Blood Plants Arthropods
Phyllostomidae
Blood Plants Arthropods Vertebrates
Phyllostomidae and the evolution of diet
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Phyllostomidae and the evolution of diet

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Presentation of my Master 1 BEE (Montpellier, France)

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Phyllostomidae and the evolution of diet

  1. 1. Curriculum vitae • Fieldwork • Labwork: The world evolutionary radiation of the cosmopolitan genus Myotis : biogeographic and temporal origins (M 2) Phyllostomidae and the evolution of diet (M 1)
  2. 2. Phyllostomidae and the evolution of diet Phylogeny & evolution of bats: evolution of diet Presented by : Yann Gager Supervised by : Emmanuel Douzery
  3. 3. Phyllostomidae Phyllostomidae and the evolution of diet
  4. 4. Phyllostomidae • Leaf-nosed bats from the New World
  5. 5. Phyllostomidae • Leaf-nosed bats from the New World • ~ 160 species described (55 genus) : More than 10% of Bats = 2nd Order in number of species after Rodents
  6. 6. Phyllostomidae • Leaf-nosed bats from the New World • ~ 160 species described (55 genus) : More than 10% of Bats = 2nd Order in number of species after Rodents • Great diversity of life-history traits : Family of Mammals with the biggest number of diet
  7. 7. Phyllostomidae Blood
  8. 8. Phyllostomidae Blood Plants
  9. 9. Phyllostomidae Blood Plants Arthropods
  10. 10. Phyllostomidae Blood Plants Arthropods Vertebrates
  11. 11. Goals of the study Phyllostomidae and the evolution of diet
  12. 12. Goals of the study • Reliable phylogenetic tree: important sampling of species and molecular data
  13. 13. Goals of the study • Reliable phylogenetic tree: important sampling of species and molecular data • Preliminary to the study of the evolution of dietdiet
  14. 14. Samplings Phyllostomidae and the evolution of diet
  15. 15. Samplings • 120 species + 3 outgroups
  16. 16. Samplings • 120 species + 3 outgroups • Compilation & concatenation of genes* : Supermatrix of 6883 aligned nucleotides *( GenBank )
  17. 17. Samplings • 120 species + 3 outgroups • Compilation & concatenation of genes* : Supermatrix of 6883 aligned nucleotides 12S 16S CO1 CYB RAG-2 *( GenBank ) 12S 16S CO1 CYB RAG-2 Species 1 X ? X ? X Species 2 X X X X X Species 3 X X X ? X Species n X X X X X
  18. 18. Phylogenetic analyses Phyllostomidae and the evolution of diet
  19. 19. Phylogenetic analyses • Maximum likelihood (GTR + Γ + INV)
  20. 20. Phylogenetic analyses • Maximum likelihood (GTR + Γ + INV) P ,MP ,M
  21. 21. Phylogenetic analyses • Maximum likelihood (GTR + Γ + INV) • Node support : Bootstrap (100 replicates)
  22. 22. Phylogenetic analyses • Maximum likelihood (GTR + Γ + INV) • Node support : Bootstrap (100 replicates) • Inference of diet : Trophic levels of the panTHERIA project* *( Jones et al. 2009 ) 1 Phytophagy 2 Omnivory 3 Animalivory
  23. 23. Evolution of diet Phyllostomidae and the evolution of diet
  24. 24. Evolution of diet • Function ACE with APE (R) : Ancestral Character Estimation Species 1 Species 2 ? Species 3 ?
  25. 25. Evolution of diet • Function ACE with APE (R) : Ancestral Character Estimation • Probabilistic model of estimation of the speed of change of the diet character state
  26. 26. Evolution of diet • Function ACE with APE (R) : Ancestral Character Estimation • Probabilistic model of estimation of the speed of change of the diet character state Species 1 Species 2 Species 3
  27. 27. Evolution of diet • Function ACE with APE (R) : Ancestral Character Estimation • Probabilistic model of estimation of the speed of change of the diet character state all changes different
  28. 28. Evolution of diet • Function ACE with APE (R) : Ancestral Character Estimation • Probabilistic model of estimation of the speed of change of the diet character state all changes different Phytophagy Omnivory Animalivory Phytophagy NA R1 R2 Omnivory R3 NA R4 Animalivory R5 R6 NA
  29. 29. Phytophagy Animalivory Omnivory
  30. 30. Phytophagy Animalivory Omnivory
  31. 31. Phytophagy Animalivory Omnivory
  32. 32. Phytophagy Animalivory Omnivory
  33. 33. Phytophagy Animalivory Omnivory
  34. 34. Evolution of diet • Specialisations, but opportunistic omnivory – Food completion
  35. 35. Evolution of diet • Specialisations, but opportunistic omnivory – Food completion – Survival when the favorite food is rare
  36. 36. Prospects Phyllostomidae and the evolution of diet
  37. 37. Prospects • To obtain a fully resolved phylogeny !
  38. 38. Prospects • To obtain a fully resolved phylogeny ! 1) More taxa
  39. 39. Prospects • To obtain a fully resolved phylogeny ! 1) More taxa 2) More genes
  40. 40. Prospects • To obtain a fully resolved phylogeny ! 1) More taxa 2) More genes 3) Both !
  41. 41. Prospects • Well supported phylogenies: Working basis for numerous research on bats!
  42. 42. Prospects • Well supported phylogenies: Working basis for numerous research on bats! Life-history traits Artibeus sp.
  43. 43. Prospects • Well supported phylogenies: Working basis for numerous research on bats! Systematics Cistugo sp.
  44. 44. Prospects • Well supported phylogenies: Working basis for numerous research on bats! Biogeography Myotis spp.
  45. 45. Prospects • Well supported phylogenies: Working basis for numerous research on bats! Conservation Craseonycteris thonglongyai
  46. 46. Acknowledgments • Team Molecular phylogeny and Evolution: E. Douzery, F. Botero, M. Ballenghien, P. Gayral, C. Delsol • Funding: ANR Mitosys 2006-2010 • Presentation design: M. David• Presentation design: M. David
  47. 47. Thank you !
  48. 48. Supermatrix • Drawbacks: Missing data e.g. artefacts • Benefits: Contribution for a phylogenetic signalsignal e.g ½ of 7kb = 3.5 kb !
  49. 49. Supermatrix 100 75 47 97 100 99 100 100 100 100 100 100 86 46 29 73 85 7395 67 85 97
  50. 50. General Time Reversible ( GTR ) A C G T A - a∏C b∏G c∏T C a∏A - d∏G e∏T • Base frequencies ∏, substitution rates (from a to f) and branch lengths G b∏A d∏C - f∏T T c∏A e∏C f∏G -
  51. 51. • Nucleotide model of evolution • General Time Reversible (GTR) with a gamma distribution of rate variation (Γ) and a proportion of invariant sites (INV) General Time Reversible + Γ + INV proportion of invariant sites (INV)
  52. 52. Evolution of diet • Matrix of rates of change of trophic level state Phytophagy Omnivory Animalivory Phytophagy NA 2,50 0 Omnivory 0,71 NA 0,69 Animalivory 0 0 NA
  53. 53. Rate change of trophic level • ER = Equal rates • SR = Synonym rates Phytophagy Omnivory Animalivory Phytophagy NA R1 R1 Omnivory R1 NA R1 Animalivory R1 R1 NA Phytophagy Omnivory Animalivory • ARD = All rates different Phytophagy Omnivory Animalivory Phytophagy NA R1 R2 Omnivory R1 NA R3 Animalivory R2 R3 NA Phytophagy Omnivory Animalivory Phytophagy NA R1 R2 Omnivory R3 NA R4 Animalivory R5 R6 NA
  54. 54. Order Chiroptera Jones and Teeling, 2006 Chiroptera
  55. 55. Phyllostomidae Blood
  56. 56. Phyllostomidae Blood Plants
  57. 57. Phyllostomidae Blood Plants Arthropods
  58. 58. Phyllostomidae Blood Plants Arthropods Vertebrates

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