estimating the reliability of a tree reconstructed phylogenetic trees are almost certainly wrong....
TRANSCRIPT
![Page 1: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/1.jpg)
Estimating the reliability of a treeReconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable are they?
![Page 2: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/2.jpg)
Reliability most of the time, ‘reliability’ refers to the topology, not to branch lengths.
reliability = probability that the members of a given clade are always members of that clade
![Page 3: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/3.jpg)
Methods phylogeneticists use different methods to test the reliability of trees
• Bootstrapping• Jackknife• Permutation tests• Likelihood ratio tests (a)LRT
![Page 4: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/4.jpg)
Bootstrapping bootstrapping uses random sampling with replacement to obtain properties of an estimator
![Page 5: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/5.jpg)
Bootstrapping bootstrapping uses random sampling with replacement to obtain properties of an estimator
![Page 6: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/6.jpg)
x
Bootstrapping bootstrapping uses random sampling with replacement to obtain properties of an estimator
xx
xx
1000-10000 times
x
f
![Page 7: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/7.jpg)
Bootstrapping in phylogenetic bootstrapping, the alignment is resampled
A A TC G CA G TT G TT C T
1ACAAG
2TCTTT
3GGGGG
4GGGGG
5GGACG
6 7TCAGA
8 9TGTTT
0ACATT
1GGGGG
4TCAGA
8TCTTT
3GGACG
6TGTTT
0ACAAG
2GGGGG
4TCTTT
9GGGGG
5
original alignment pseudo alignment
![Page 8: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/8.jpg)
Bootstrapping
A B C D E F A C B D E F
original tree bootstrapped tree
+1
+1+1
+1
+1+1
+1+0
+1+1
![Page 9: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/9.jpg)
A C B D E FA C B D E F
A C B D E FA C B D E F
Bootstrapping
A B C D E F A C B D E F
original tree bootstrapped trees
0.810.75
0.87
0.95
0.800.90
0.50.47
0.450.23
![Page 10: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/10.jpg)
Jackknife methods the Jackknife procedure uses random sampling without replacement to obtain properties of an estimator
![Page 11: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/11.jpg)
Jackknife methods the Jackknife procedure uses random sampling without replacement to obtain properties of an estimator
![Page 12: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/12.jpg)
Permutation methods Permutation tests are standard in non-parametric statistics. They reorder the data to obtain a null distribution.
![Page 13: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/13.jpg)
Permutation methods Permutation tests are standard in non-parametric statistics. They reorder the data to obtain a null distribution.
N=18, x=20 N=10, x=25 Dif=5
![Page 14: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/14.jpg)
Permutation methods
N=18, x=23 N=10, x=19.6 Dif=3.4
![Page 15: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/15.jpg)
Permutation methods
difference
f
5% largest differences5% smallest differences
actual difference
![Page 16: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/16.jpg)
Permutation methods in phylogenetics, species can be permuted within characters
A A TC G CA G TT G TT C T
1ACAAG
2TCTTT
3GGGGG
4GGGGG
5GGACG
6 7TCAGA
8 9TGTTT
0species 1
species 2
species 3
species 4
species 5
ACATT
1
A
C
AT
T
1
reshuffle
![Page 17: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/17.jpg)
Permutation methods in phylogenetics, species can be permuted within characters
A A TC G CA G TT G TT C T
1ACAAG
2TCTTT
3GGGGG
4GGGGG
5GGACG
6 7TCAGA
8 9TGTTT
0species 1
species 2
species 3
species 4
species 5
A
C
AT
T
1
AC
A
AG2
ACAAG
2
reshuffle
![Page 18: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/18.jpg)
Permutation methods in phylogenetics, species can be permuted within characters
A A TC G CA G TT G TT C T
1ACAAG
2TCTTT
3GGGGG
4GGGGG
5GGACG
6 7TCAGA
8 9TGTTT
0species 1
species 2
species 3
species 4
species 5
A
C
AT
T
1
AC
A
AG2
A
TG
CG
TG T
CT
T
C
TT
T
3GGGGG
4GGGGG
5
G
GA
C
G
6 7TCA
GA
8 9
T
G
TT
T0
![Page 19: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/19.jpg)
Likelihood ratio tests
A B C D E F G H I J K L
X (ABCDEF) Y (GHI)
W (J)Z (KL)
![Page 20: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/20.jpg)
Likelihood ratio tests standard likelihood tests compare trees with and without the branch
X (ABCDEF) Y (GHI)
W (J)Z (KL)
X Y
WZ
Likelihood = L1 Likelihood = L0
probability that branch exists = 2 * [ln L1 – ln L0]
![Page 21: Estimating the reliability of a tree Reconstructed phylogenetic trees are almost certainly wrong. They are estimates of the true tree. But how reliable](https://reader034.vdocuments.net/reader034/viewer/2022051516/56649cb95503460f94981004/html5/thumbnails/21.jpg)
Approximate likelihood ratio test aLRT is fast, accurate and powerful
X Y
WZ
Likelihood = L1
Likelihood = L2
approximate probability that branch exists = 2 * [ln L1 – ln L2]
X Z
WY
Likelihood = L3
X Z
YW