Presentation of my Master 1 BEE (Montpellier, France)

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. Phyllostomidae and the
evolution of diet
Phylogeny & evolution of bats:
evolution of diet
Presented by : Yann Gager
Supervised by : Emmanuel Douzery

3. Phyllostomidae
Phyllostomidae and the evolution of diet

4. Phyllostomidae
• Leaf-nosed bats from the New World

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. 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. Phyllostomidae
Blood

8. Phyllostomidae
Blood Plants

9. Phyllostomidae
Blood Plants Arthropods

10. Phyllostomidae
Blood Plants Arthropods Vertebrates

11. Goals of the study
Phyllostomidae and the evolution of diet

12. Goals of the study
• Reliable phylogenetic tree:
important sampling of species
and molecular data

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. Samplings
Phyllostomidae and the evolution of diet

15. Samplings
• 120 species + 3 outgroups

16. Samplings
• 120 species + 3 outgroups
• Compilation & concatenation of genes* :
Supermatrix of 6883 aligned nucleotides
*( GenBank )

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. Phylogenetic analyses
Phyllostomidae and the evolution of diet

19. Phylogenetic analyses
• Maximum likelihood (GTR + Γ + INV)

20. Phylogenetic analyses
• Maximum likelihood (GTR + Γ + INV)
P ,MP ,M

21. Phylogenetic analyses
• Maximum likelihood (GTR + Γ + INV)
• Node support : Bootstrap (100 replicates)

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. Evolution of diet
Phyllostomidae and the evolution of diet

24. Evolution of diet
• Function ACE with APE (R) :
Ancestral Character Estimation
Species 1
Species 2
?
Species 3
?

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. 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. 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. 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. Phytophagy
Animalivory
Omnivory

30. Phytophagy
Animalivory
Omnivory

31. Phytophagy
Animalivory
Omnivory

32. Phytophagy
Animalivory
Omnivory

33. Phytophagy
Animalivory
Omnivory

34. Evolution of diet
• Specialisations, but opportunistic omnivory
– Food completion

35. Evolution of diet
• Specialisations, but opportunistic omnivory
– Food completion
– Survival when the favorite food is rare

36. Prospects
Phyllostomidae and the evolution of diet

37. Prospects
• To obtain a fully resolved phylogeny !

38. Prospects
• To obtain a fully resolved phylogeny !
1) More taxa

39. Prospects
• To obtain a fully resolved phylogeny !
1) More taxa
2) More genes

40. Prospects
• To obtain a fully resolved phylogeny !
1) More taxa
2) More genes
3) Both !

41. Prospects
• Well supported phylogenies:
Working basis for numerous research on bats!

42. Prospects
• Well supported phylogenies:
Working basis for numerous research on bats!
Life-history
traits
Artibeus sp.

43. Prospects
• Well supported phylogenies:
Working basis for numerous research on bats!
Systematics
Cistugo sp.

44. Prospects
• Well supported phylogenies:
Working basis for numerous research on bats!
Biogeography
Myotis spp.

45. Prospects
• Well supported phylogenies:
Working basis for numerous research on bats!
Conservation
Craseonycteris thonglongyai

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. Thank you !

49. Supermatrix
• Drawbacks: Missing data
e.g. artefacts
• Benefits: Contribution for a phylogenetic
signalsignal
e.g ½ of 7kb = 3.5 kb !

50. Supermatrix
100
75
47
97
100
99
100
100
100
100
100
100
86
46
29
73
85
7395
67
85
97

51. 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 -

52. • 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)

53. 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

54. 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

55. Order
Chiroptera
Jones and Teeling, 2006
Chiroptera

56. Phyllostomidae
Blood

57. Phyllostomidae
Blood Plants

58. Phyllostomidae
Blood Plants Arthropods

59. Phyllostomidae
Blood Plants Arthropods Vertebrates