Overview of the approaches I co-developed to reconstruct species trees and gene trees, in the presence of gene duplications, losses and transfers, or incomplete lineage sorting. Includes Phyldog, ALE, MP-EST*, RevBayes.

1. Bastien Boussau
LBBE, CNRS, Université de Lyon
Genome-scale phylogenomics

2. Collaborators
• Lyon collaborators:
• Adrián Arellano Davín
• Gergely Szöllősi (Budapest),
• Eric Tannier,
• Vincent Daubin,
• Thomas Bigot,
• Magali Semeria,
• Manolo Gouy,
• Laurent Duret
• Austin collaborators:
• Siavash Mirarab
• Md. Shamsuzzoha Bayzid
• Tandy Warnow
• RevBayes collaborators:
• Sebastian Hoehna
• Michael Landis
• Tracy Heath
• Fredrik Ronquist
• Brian Moore
• John Huelsenbeck
• …

3. To study genome evolution:
1. One species tree:
!
!
!
2. Thousands of gene trees:
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E

4. To study genome evolution:
1. One species tree:
!
!
!
2. Thousands of gene trees:
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E

5. Why our current pipeline can be improved

6. Why our current pipeline can be improved
•Gene alignments:
•Error prone
•Short
•Point estimates

7. Why our current pipeline can be improved
•Gene alignments:
•Error prone
•Short
•Point estimates
•Gene trees:
•based on alignments
•Point estimates

8. Why our current pipeline can be improved
•Gene alignments:
•Error prone
•Short
•Point estimates
•Gene trees:
•based on alignments
•Point estimates
•Species trees:
•based on gene trees

9. Why our current pipeline can be improved
•Gene alignments:
•Error prone
•Short
•Point estimates
•Gene trees:
•based on alignments
•Point estimates
•Species trees:
•based on gene trees

10. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E

11. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E

12. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E

13. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
D

14. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
D DL

15. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGTD DL

16. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGT ILSD DL

17. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGT ILS
DL: Boussau et al., Genome Research 2013
D DL

18. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGT ILS
DL: Boussau et al., Genome Research 2013
D DL
DL+T:!
Szöllősi et al. "
PNAS 2013

19. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGT ILS
ILS: !
Mirarab et al.
Science 2014
DL: Boussau et al., Genome Research 2013
D DL
DL+T:!
Szöllősi et al. "
PNAS 2013

20. (thousands of alignments)
PHYLDOG
All gene families
Rooted species tree,
numbers of duplications
and losses,
rooted gene trees D1
D2
D3
D4
D5
D6
L2
L1
L4
L3
L5
L6
Joint reconstruction of
the species tree,
gene trees, and
numbers of duplications and losses
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
D1
D3
D2 D4
D5 D6
L1
L3
L2 L4
L5 L6
Boussau et al., Genome Research 2013

21. (thousands of alignments)
PHYLDOG
All gene families
Rooted species tree,
numbers of duplications
and losses,
rooted gene trees D1
D2
D3
D4
D5
D6
L2
L1
L4
L3
L5
L6
Joint reconstruction of
the species tree,
gene trees, and
numbers of duplications and losses
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
D1
D3
D2 D4
D5 D6
L1
L3
L2 L4
L5 L6
Probabilistic models:
• sequence evolution
• gene family evolution
Boussau et al., Genome Research 2013

22. Sus scrofa
Felis catus
Ornithorhynchus anatinus
Oryctolagus cuniculus
Loxodonta africana
Mus musculus
Gorilla gorilla
Dipodomys ordii
Monodelphis domestica
Vicugna pacos
Macaca mulatta
Tupaia belangeri
Procavia capensis
Spermophilus tridecemlineatus
Pongo pygmaeus
Tursiops truncatus
Microcebus murinus
Callithrix jacchus
Equus caballus
Erinaceus europaeus
Tarsius syrichta
Choloepus hoffmanni
Ochotona princeps
Cavia porcellus
Pan troglodytes
Bos taurus
Rattus norvegicus
Homo sapiens
Otolemur garnettii
Dasypus novemcinctus
Echinops telfairi
Pteropus vampyrus
Macropus eugenii
Canis familiaris
Sorex araneus
Myotis lucifugus
Laurasiatheria
Afrotheria
Xenarthra
Marsupials
Primates
Glires
010000
010000
010000
010000
010000
010000
010000
PHYLDOG
TreeBeST
PhyML
PHYLDOG: better trees for better ancestral genomes

23. An example gene family
0.1
Ornithorhynchus anatinus
0.3
Ornithorhynchus anatinus
Mus musculus
Mus musculus
Mus musculus
Cavia porcellus
Mus musculus
Oryctolagus cuniculus
Canis familiaris
Bos taurus
Homo sapiens
Pongo pygmaeus
Oryctolagus cuniculus
Cavia porcellus
Equus caballus
Equus caballus
Bos taurus
Callithrix jacchus
Homo sapiens
Monodelphis domestica
Spermophilus tridecemlineatus
Homo sapiens
Ornithorhynchus anatinus
Ornithorhynchus anatinus
Ornithorhynchus anatinus
Ornithorhynchus anatinus
Mus musculus
Mus musculus
Ornithorhynchus anatinus
Ornithorhynchus anatinus
Mus musculus
Mus musculus
Mus musculus
Cavia porcellus
Mus musculus
Oryctolagus cuniculus
Canis familiaris
Bos taurus
Homo sapiens
Pongo pygmaeus
Oryctolagus cuniculus
Cavia porcellus
Equus caballus
Equus caballus
Bos taurus
Callithrix jacchus
Homo sapiens
Monodelphis domestica
Spermophilus tridecemlineatus
Homo sapiens
Ornithorhynchus anatinus
Ornithorhynchus anatinus
Ornithorhynchus anatinus
Ornithorhynchus anatinus
Mus musculus
Mus musculus
TreeBeST PHYLDOG
Boussau et al., Genome Research 2013

24. Species: A B C D
T
I
M
E
ILS: !
Mirarab et al.
Science 2014
DL: Boussau et al., Genome Research 2013
DL+T:!
Szöllősi et al. "
PNAS 2013

25. Species: A B C D
T
I
M
E
LGT ILS
ILS: !
Mirarab et al.
Science 2014
DL: Boussau et al., Genome Research 2013
D DL
DL+T:!
Szöllősi et al. "
PNAS 2013

26. Gene transfers and the quixotic pursuit of the TOL
Doolittle WF,
Science 1999

27. Gene transfers and the quixotic pursuit of the TOL
Doolittle WF,
Science 1999

28. Gene transfers and the quixotic pursuit of the TOL
Doolittle WF,
Science 1999
“The monistic concept of a single universal tree appears […]
increasingly obsolete. […][It is] no longer the most
scientifically productive position to hold[…][It] accounts for
only a minority of observations from genomes.”!
Bapteste, O’Malley, Beiko, Ereshefsky, Gogarten, Franklin-Hall,
Lapointe, Dupré, Dagan, Boucher, Martin, !
Biology Direct 2009.

29. Using transfers to date clades
?
T
I
M
E

30. Using transfers to date clades
?
T
I
M
E

31. Using transfers to date clades
?
T
I
M
E

32. Using transfers to date clades
?
T
I
M
E

33. Using transfers to date clades
?
T
I
M
E

34. Using transfers to date clades
?
T
I
M
E

35. Using transfers to date clades
?
T
I
M
E
Because we can identify gene transfers, we have information for
ordering the nodes of a species tree

36. Bayesian species tree inference
accounting for DTL events
• STRALE:
• A Bayesian probabilistic method that can interpret thousands of
gene trees in terms of:
• speciation events
• duplication events (D)
• transfer events (T)
• loss events (L)
• A method able to estimate the DTL rates
• A method able to reconstruct the species tree
• A method able to order the nodes of the species tree

37. Simulation to test the species tree reconstruction
• 20 species
• 200 gene families
1 5
1
3
1 4
1 0
6
8
1 2
1 8
1 3
5
4
2
9
0
1 1
1 9
7
1 6
1 7
2
1 3
7
1 7
1 5
1
5
1 2
1 0
1 6
1 1
9
0
4
8
3
1 4
1 9
6
1 8
Simulated Inferred

38. Better gene trees, fewer transfers
Usual
approach
ALE
+DTL
RFdistancetorealtree
Szöllősi et al., Syst. Biol. 2013

39. Better gene trees, fewer transfers
Usual
approach
ALE
+DTL
Transfereventsperfamily
Usual
approach
ALE
+DTL
RFdistancetorealtree
Szöllősi et al., Syst. Biol. 2013

40. Better gene trees, fewer transfers
Usual
approach
ALE
+DTL
Transfereventsperfamily
Usual
approach
ALE
+DTL
RFdistancetorealtree
Szöllősi et al., Syst. Biol. 2013
Better ancestral genomes:
go see Adrián Arellano Davín’s poster on
reconstructing ancestral genomes across the
tree of life!

41. Species: A B C D
T
I
M
E
ILS: !
Mirarab et al.
Science 2014
DL: Boussau et al., Genome Research 2013
DL+T:!
Szöllősi et al. "
PNAS 2013

42. Species: A B C D
T
I
M
E
LGT ILS
ILS: !
Mirarab et al.
Science 2014
DL: Boussau et al., Genome Research 2013
D DL
DL+T:!
Szöllősi et al. "
PNAS 2013

43. 18
Statistical binning
Mirarab et al., Science 2014

44. 18
Statistical binning
Mirarab et al., Science 2014
MP-EST

45. 19
Statistical binning
Mirarab et al., Science 2014
MP-EST

46. 19
Statistical binning
Mirarab et al., Science 2014
MP-EST
MP-EST

47. 20
Statistical binning
improves
species tree inference
Mirarab et al., Science 2014

48. 21
Statistical binning
Mirarab et al., Science 2014

49. 22
Jarvis et al., Science 2014
Statistical binning and birds

50. RevBayes
• Collaborative effort
• Model-based phylogenetics
• Many models of sequence evolution
• Models for dating
• Models for phylogeography
• Models for continuous traits
• Models for gene tree/species tree inference
• http://revbayes.net
• Sebastian Hoehna
• Michael Landis
• Tracy Heath
• Fredrik Ronquist
• Nicolas Lartillot
• Brian Moore
• John Huelsenbeck
• …

51. Conclusions
• We develop methods for gene tree and species
tree inference
• Improvement of gene trees and species trees in
the presence of:
• duplications and losses,
• transfers,
• incomplete lineage sorting
• Parallel algorithms applicable to genome-scale
data

52. Thanks!
• Lyon collaborators:
• Adrián Arellano Davín
• Gergely Szöllősi (Budapest),
• Eric Tannier,
• Vincent Daubin,
• Thomas Bigot,
• Magali Semeria,
• Manolo Gouy,
• Laurent Duret
• Austin collaborators:
• Siavash Mirarab
• Md. Shamsuzzoha Bayzid
• Tandy Warnow

53. Thanks!
• Lyon collaborators:
• Adrián Arellano Davín
• Gergely Szöllősi (Budapest),
• Eric Tannier,
• Vincent Daubin,
• Thomas Bigot,
• Magali Semeria,
• Manolo Gouy,
• Laurent Duret
• Austin collaborators:
• Siavash Mirarab
• Md. Shamsuzzoha Bayzid
• Tandy Warnow
Go see Adrián Arellano
Davín’s poster on
reconstructing ancestral
genomes across the tree
of life!