total evidence phylogenies: the missing data issue
TRANSCRIPT
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Total evidence phylogenies
The missing data issue
Thomas Guillerme
? @TGuillerme
Trinity College Dublin
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Acknowledgements
Natalie Cooper (Natural History Museum - UK)
Gavin Thomas (Univ. Sheffield - UK)
Emmanuel Douzery (Univ. Montpellier II - FR)
Frédéric Delsuc (Univ. Montpellier II - FR)
Trevor Hodkinson (Trinity College Dublin - IE)
@TGuillerme
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Time
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A T T G A A C A T C G A A C A T C G G A C A T C G G A A
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0 0 1 0 0 1 1 1 0 1 1 0 0 1 1 0
A T T G A A C A T C G A A C A T C G G A C A T C G G A A
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? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C A T C G A A C A T C G G A C A T C G G A A
0 0 1 0 0 1 1 1 0 1 1 0 0 1 1 0 1 0 0 0 0 1 1 0 0 0 1 1 0 1 1 1
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? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C A T C G A A C A T C G G A C A T C G G A A
0 0 1 0 0 1 1 1 0 1 1 0 0 1 1 0 1 0 0 0 0 1 1 0 0 0 1 1 0 1 1 1
? ? ? ? ? ? ? ?
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What is the effect of missing data on tree
topology?
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? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
0 0 1 0
0 1 1 1
0 1 1 0
0 1 1 0
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
No missing data
Missing data
25%
50%
75%
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
? ? ? ?
0 1 1 1
0 1 1 0
0 1 1 0
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
0 0 1 0
? ? ? ?
0 1 1 0
? ? ? ?
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
? ? ? ?
? ? ? ?
? ? ? ?
0 1 1 0
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C A T C G A A C A T C G G A C A T C G G A A
0 0 1 0 0 1 1 1 0 1 1 0 0 1 1 0 1 0 0 0 0 1 1 0 0 0 1 1 0 1 1 1
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C A T C G A A C A T C G G A C A T C G G A A
0 0 1 0 0 1 1 1 0 1 1 0 0 1 1 0 ? 0 ? 0 0 1 ? 0 ? ? 1 ? 0 ? 1 1
Fossil taxa
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C A T C G A A C A T C G G A C A T C G G A A
? ? ? ? 0 1 1 1 ? ? ? ? ? ? ? ? 1 0 0 0 0 1 1 0 0 0 1 1 0 1 1 1
Living taxa
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
0 0 1 0
0 1 1 1
0 1 1 0
0 1 1 0
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
No missing data
Missing data
25%
50%
75%
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
? ? ? ?
0 1 1 1
0 1 1 0
0 1 1 0
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
0 0 1 0
? ? ? ?
0 1 1 0
? ? ? ?
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
? ? ? ?
? ? ? ?
? ? ? ?
0 1 1 0
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
A B C D
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
0 0 1 0
0 1 1 1
0 1 1 0
0 1 1 0
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
No missing data
Missing data
25%
50%
75%
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
? ? ? ?
0 1 1 1
0 1 1 0
0 1 1 0
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
0 0 1 0
? ? ? ?
0 1 1 0
? ? ? ?
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
? ? ? ?
? ? ? ?
? ? ? ?
0 1 1 0
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
A B C D
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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150 CPU years later…
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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6 PhD months later…
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
0 0 1 0
0 1 1 1
0 1 1 0
0 1 1 0
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
No missing data
Missing data
25%
50%
75%
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
? ? ? ?
0 1 1 1
0 1 1 0
0 1 1 0
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
0 0 1 0
? ? ? ?
0 1 1 0
? ? ? ?
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C
A T C G A A C
A T C G G A C
A T C G G A A
? ? ? ?
? ? ? ?
? ? ? ?
0 1 1 0
1 0 0 0
0 1 1 0
0 0 1 1
0 1 1 1
Sim
ula
ted
Da
ta
A B C D
A B C D
A B C D
A B C D
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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A B C D
A B C D
A B C D
A B C D
No missing data
Missing data
25%
50%
75%
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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Tre
e s
imila
rity
Data
1
0
100% 25% Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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Tre
e s
imila
rity
1
0
Trees are identical
Trees are no more different than expected by chance
Data 100% 25% Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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Results
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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Tre
e s
imila
rity
1
0
Missing data in the fossil record
Data 100% 25% Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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Tre
e s
imila
rity
1
0
Missing data in the fossil record
Missing data for living taxa
Data 100% 25% Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C A T C G A A C A T C G G A C A T C G G A A
0 0 1 0 0 1 1 1 0 1 1 0 0 1 1 0 1 0 0 0 0 1 1 0 0 0 1 1 0 1 1 1
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C A T C G A A C A T C G G A C A T C G G A A
0 0 1 0 0 1 1 1 0 1 1 0 0 1 1 0 1 0 0 0 0 ? 1 0 0 0 1 1 0 1 1 1
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
? ? ? ? ? ? ?
A T T G A A C A T C G A A C A T C G G A C A T C G G A A
0 0 1 0 0 1 1 1 ? ? ? ? 0 1 1 0 1 0 0 0 0 ? 1 0 0 0 1 1 0 1 1 1
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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We need morphological data
from living taxa!
Guillerme & Cooper, accepted, Mol. Phyl. Evol.
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How much data are out there?
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Guillerme & Cooper, 2015, bioRxiv
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Guillerme & Cooper, 2015, bioRxiv
Available data
?
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Guillerme & Cooper, 2015, bioRxiv
Available data
?
![Page 37: Total evidence phylogenies: the missing data issue](https://reader036.vdocument.in/reader036/viewer/2022062503/58ee32261a28abe55f8b4687/html5/thumbnails/37.jpg)
Guillerme & Cooper, 2015, bioRxiv
Available data
![Page 38: Total evidence phylogenies: the missing data issue](https://reader036.vdocument.in/reader036/viewer/2022062503/58ee32261a28abe55f8b4687/html5/thumbnails/38.jpg)
Guillerme & Cooper, 2015, bioRxiv
Available data
![Page 39: Total evidence phylogenies: the missing data issue](https://reader036.vdocument.in/reader036/viewer/2022062503/58ee32261a28abe55f8b4687/html5/thumbnails/39.jpg)
Guillerme & Cooper, 2015, bioRxiv
Available data
16% 56/351
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Tre
e s
imila
rity
1
0
Missing data in the fossil record
Missing data for living taxa
Data 100% 25%
![Page 41: Total evidence phylogenies: the missing data issue](https://reader036.vdocument.in/reader036/viewer/2022062503/58ee32261a28abe55f8b4687/html5/thumbnails/41.jpg)
Tre
e s
imila
rity
1
0
Missing data in the fossil record
Missing data for living taxa
Data 100% 25%
![Page 42: Total evidence phylogenies: the missing data issue](https://reader036.vdocument.in/reader036/viewer/2022062503/58ee32261a28abe55f8b4687/html5/thumbnails/42.jpg)
Tre
e s
imila
rity
1
0
Missing data in the fossil record
Missing data for living taxa
Data 100% 25%
@TGuillerme
Guillerme & Cooper, 2015 biorxiv.org
Guillerme & Cooper, accepted Mol. Phyl. Evol.
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Tre
e s
imila
rity
1
0
Missing data in the fossil record
Missing data for living taxa
Data 100% 25%
@TGuillerme
Thank you Guillerme & Cooper, 2015
biorxiv.org
Guillerme & Cooper, accepted Mol. Phyl. Evol.