chap. 6 inferring molecular phylogeny - amborella.netamborella.net/2014-molecular...
TRANSCRIPT
![Page 1: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/1.jpg)
Chap. 6Inferring Molecular Phylogeny
![Page 2: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/2.jpg)
- Basic process to reconstruct phylogenetic treeSequencing search filtering alignments phylogenetic analyses phylogenetic tree (tree network) rooting
Data for Molecular Phylogenetics- DNA-DNA hybridization (%)- Restriction Fragment Length Polymorphism (RFLP) (0/1)- Single gene comparison (A, C, G, T + gene structure)- Multiple gene comparison ( “ )- Comparative genomics ( “ )- Protein sequence comparison (20 amino acids)
Whatever it is, we can transfer them into binary (0/1) data.
1TTTTT
2CAAAA
3AAAAT
4CCTTT
5CCCAA
6TGGGG
ABCDE
1A
00000
1C
00000
1G
00000
1T
11111
2A
01111
2C
10000
2G
00000
2T
00000
3A
11110
3C
00000
3G
00000
3T
00001
4A
00000
4C
11000
4G
00000
4T
00111
. . .
ABCDE
An example of data transformation
![Page 3: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/3.jpg)
Distances vs. Discrete characters
![Page 4: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/4.jpg)
An example for comparing Character-based Method and Distance-based Method
“Phenetics vs. Phylogenetics” in Rordford et al.
![Page 5: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/5.jpg)
I. Character-based method: Maximum Parsimony (MP)in case of ordered characters
When the character is ordered, we can make phylogenetic tree using the following method- ordered: 0 1 2
1) Make distance matrix
2) Choose minimum distance from ANC
![Page 6: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/6.jpg)
c.f.) HTU: Hypothetical Taxonomic Unit
3) Set HTU1 and find minimum distanced taxa from HTU1
![Page 7: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/7.jpg)
4) Reconstruct character status of HTU1 and add HTU1 in the matrix and distance table
![Page 8: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/8.jpg)
5) Set HTU2 and find minimum distanced taxa again and repeat 3)~4).
![Page 9: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/9.jpg)
DELTRAN (DElayed TRANsformation) optimization : character changes are placed at terminals in the tree
ACCTRAN (ACCelerated TRANsformation) optimization:character changes are placed at the base rather than terminals.
6) Now we got a tree and we may reconstruct character evolution. There are two different optimization method:
![Page 10: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/10.jpg)
II. Distance-based Method: neighbor joining (NJ), UPGMA…fast and easy
1) Calculate coefficient of overall similarity whatever the method is.
2) Choose the most similar pair and link them
![Page 11: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/11.jpg)
3) Combine two taxa and named “P”.
4) Calculate similarity between P and others
6) Repeat 2), 3) 4).
Now, we have both trees from the theories of pheneticsand cladistics (phylogenetics). Note: two trees may have different topology.
![Page 12: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/12.jpg)
1
T
C
C
A
2
T
C
C
A
3
T
C
C
A
4
T
C
C
A
5
G
G
G
C
6
C
C
A
A
A
B
C
D
Another example: Distance based method (phenetics) vs. Character based method (cladistics)
![Page 13: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/13.jpg)
1
T
C
C
A
2
T
C
C
A
3
T
C
C
A
4
T
C
C
A
5
G
G
G
C
6
C
C
A
A
A
B
C
D
2 1 0
5 0
1
-
-
-
-
A B C D
A
B
C
D
similarity matrix
5
B C
5
X
X=B+C
X C C C C G C/A
1.5 0
0.5
-
-
-
A X D
A
X
D
1.5
1.5
A
Y
Y=X+A
Y T/C T/C T/C T/C G C/C/A
Y D
Y
D
0.33-
-
0.33
0.33
D
Distance based method (phenetics)
Set similarity coefficient = number of matching characters
![Page 14: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/14.jpg)
1
T
C
C
A
2
T
C
C
A
3
T
C
C
A
4
T
C
C
A
5
G
G
G
C
6
C
C
A
A
A
B
C
D
Character based method (cladistics); parsimony
![Page 15: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/15.jpg)
A B
C
Unrooted Rooted
A B C A C B C B AN=3
N=4
N=n…
A
B
C
D
A
C
B
D
A
D
C
B
A B C D A D B C A D B C A B D C A B D C
A C B D A D C B A D C B A C D B A C D B
C B A D C B D A C D B A C B D A C B D A
![Page 16: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/16.jpg)
Fig. 26-15-4
Species I
Site
Species II
Species III
I
II
III
I
III
IIIII
III
Ancestralsequence
1/C1/C
1/C
1/C
1/C
4321
C
C C
C
T
T
T
T
T
T A
AA
A G
G
I I
I
II
II
II
III
III
III3/A
3/A
3/A3/A
3/A
2/T2/T
2/T 2/T
2/T4/C
4/C
4/C
4/C
4/C
I I
I
II
II
II
III
III
III
7 events7 events6 events
Species I
Three phylogenetic hypotheses:
Species II Species III
I
II
III
I
III
IIIII
III
![Page 17: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/17.jpg)
1
T
C
C
A
2
T
C
C
A
3
T
C
C
A
4
T
C
C
A
5
G
G
G
C
6
C
C
A
A
A
B
C
D
Character based method (cladistics); parsimony
A
B
C
D
I
A
C
B
D
II
A
D
C
B
III
10 changes
11 changes
11 changes
![Page 18: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/18.jpg)
Distance based method (phenetics)
B C
5
1.5
A
0.33
D
Character based method (cladistics); parsimony
A
B
C
D
B A C D
B
C
D
A
1 step
![Page 19: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/19.jpg)
1TTTTT
2CAAAA
3AAAAT
4CCTTT
5CCCAA
6TGGGG
ABCDE
Uninformative character: 1, 2, 3, 6
Variable character: 2, 3, 4, 5, 6
Informative character: 4, 5
Character-based method (parsimony): using ONLY informative charactersDistance method: using all characters
![Page 20: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/20.jpg)
Distances vs. Discrete characters
![Page 21: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/21.jpg)
A B
C
Unrooted Rooted
A B C A C B C B AN=3
N=4
N=n…
A
B
C
D
A
C
B
D
A
D
C
B
A B C D A D B C A D B C A B D C A B D C
A C B D A D C B A D C B A C D B A C D B
C B A D C B D A C D B A C B D A C B D A
![Page 22: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/22.jpg)
Character-based Method of Phylogenetics
Parsinomy: Parsimony is a non-parametric statistical method commonly used in computational phylogenetics for estimating phylogenies. Under parsimony, the preferred phylogenetic tree is the tree that requires the least evolutionary change to explain some observed data.
STRATEGIES FOR FASTER SEARCH1) Exhaustive search: search all possible trees
It is NOT applicable method in most cases
![Page 23: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/23.jpg)
2) Branch-and-bound method
i) Select three taxa randomlyii) Add taxa one by oneiii) Choose only trees
having minimum stepsiv) Repeat i)~iii) with different
three randomly selected taxa
v) Finally select tree(s)having minimum stepsin the trees we selected in each repeat.
5 steps
9 steps
7 steps
7 steps
12 steps15 steps12 steps
12 steps
17 steps
10 steps10 steps
10 steps
10 steps
10 steps
Calculation of 20 taxa:about 1021 trees
Still NOT applicable method in most cases
![Page 24: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/24.jpg)
3) Heuristic search I
- Make random tree first and randomly prune and graft.
- Choose minimum stepped tree- Try another prune and graft…
- Most frequently used in the sequence analyses.
Branch swapping
![Page 25: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/25.jpg)
3) Heuristic search II
Star decomposition- Make a star tree first- Make several different nodes- Choose minimum stepped tree- Make different nodes…
![Page 26: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/26.jpg)
In the heuristic search, we should repeat the analyses several times with different starting point to find “different tree islands”.
![Page 27: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/27.jpg)
Rooting
• When we analyze phylogeney of certain group, the
“outgroup” should be included in the data matrix.
• Generally, “sister group” is used as outgroup.
• The preliminary result of phylogenetic analysis is always
unrooted tree. After setting a rooting position the tree will
be a rooted tree sho.wing evolutionary history.
• A node of outgroup(s) will be a rooting position.
![Page 28: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/28.jpg)
Address Tree Confidence1) Bootstrapping2) Jackknifing3) Decay analysis
Bootstrapping: i) Make resampled pseudo-matricesii) Analyze each pseudo-matrix
and choose the best tree in each pseudo-matrix
iii) Check the % of nodes formedin the trees from eachpseudo-matrix
100%
66.6%
![Page 29: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/29.jpg)
Remember! Consensus Tree- Strict consensus tree- semistrict consensus tree- 50% majority rule consensus tree
![Page 30: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/30.jpg)
Tree confidence- Bootstrapping- Jackknifing- Decay analysis
Jackknifing
1TTTTT
2CAAAA
3AAAAT
4CCTTT
5CCCAA
6TGGGG
ABCDE
Original matrix
1TTTTT
3AAAAT
4CCTTT
6TGGGG
ABCDE
1TTTTT
2CAAAA
3AAAAT
4CCTTT
ABCDE
3AAAAT
4CCTTT
5CCCAA
6TGGGG
ABCDE
Submatrix 1 Submatrix 2 Submatrix 3 ···
···
Tree 1 Tree 2 Tree 3
Consensus tree
![Page 31: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/31.jpg)
Tree confidence- Bootstrapping- Jackknifing- Decay analysis
Michelia cavalerieiM. pealiana
Michelia bailloniiMichelia champ
Michelia odoraMichelia figo
E.ovalisMichelia cathcartii
M. elegansM. biondii
M. kobusM. dawsoniana
M. campbelliiM. denudataM. cylindrica
M. acuminataM. sinica
Pachylarnax praecalvaM. nitida
M. panamensisM. virginiana
M. tamaulipanaM. grandiflora
M. guatemalensisKmeria duperreanaKmeria septentrionalis
Manglietia grandManglietia aroma
Manglietia coniferaManglietia glauca
M. officinalisM. tripetala
M. sieboldiiM. wilsonii
M. fraseri var. fraseriM. fraseri var. pyramidata
M. macrophyllaM. dealbata
M. cocoM. gigantifolia
M. henryiM. pterocarpaM. liliifera
M. splendensM. mexicana
M. dodecapetalaLiriodendron chinense
Liriodendron tulipifera
256 steps: 1 tree257 steps: 5 trees258 steps: 83 trees259 steps: 345 trees … …
Strict consensus tree
Recognize “collepsed” node
D1
… D2… D3
Decay analysis
![Page 32: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/32.jpg)
A B C D E F A B C D E F
Short terminal branches Long terminal branches
Which one is more difficult to reconstruct their phylogeney?
Time
Divergence Divergence
Time
![Page 33: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/33.jpg)
Long-branch attraction is always a problem in the phylogenetic analyses!
![Page 34: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/34.jpg)
Long Branch Attraction
A B
C
True Phylogeny: 21 steps
A B
C
Tree Generated by Parsimony Analysis:20 steps
Homoplasious characters(parallelisms)
Homoplasious character
a phenomenon in phylogenetic analyses (most commonly those employing maximum parsimony) when rapidly evolving lineages are inferred to be closely related, regardless of their true evolutionary relationships.
ABCANC
TGGG
CCAA
GACC
ATTT
TTCA
TTCC
TACG
ATTT
CTCC
GGGA
CTCC
TTCT
TCCC
CTCT
TCCC
TTTA
TCCC
TATT
ATTT
TGTT …
ANCANC
![Page 35: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/35.jpg)
How can we minimize long-branch attraction?
1) Add additional taxa then long-branches will break up.2) Use proper analysis method NOT parsimony, neighbor-joining but “maximum likelihood”
Based on the description in Campbell et al. (General Biology, Chap. 26):
The principle of maximum likelihood states that given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events.
![Page 36: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/36.jpg)
Human
15%
Tree 1: More likely Tree 2: Less likely
(b) Comparison of possible trees
15% 15%
5%
5%
10%
25%20%
40%
40%
30%0
0
0
(a) Percentage differences between sequences
Human Mushroom
Mushroom
Tulip
Tulip
Maximum Likelihood
![Page 37: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/37.jpg)
Maximum likelihood method: evaluates the probability that the chosen evolutionary model will have generated the observed sequences (the probability of the data under the model); phylogenies are then inferred by finding those trees that yield the highest likelihoods.
For various trees (various topologies), we have to find a tree maximizing likelihood value. normally use log likelihood.
하나의 tree에 대하여 site 당 염기가 진화할 수있는 모든 확률의 합을 계산하고 이를 모든 site에서 계산하여 합친 값을 구한다. Likelihood값을최대화한 한 개의 tree를 찾아냄
![Page 38: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/38.jpg)
Who can minimize long-branch attraction?
![Page 39: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/39.jpg)
http://www.youtube.com/watch?v=H6IrUUDboZo
• Tree of Life Project(ToL): http://tolweb.org/tree/• KToL: Korean Tree of Life
![Page 40: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/40.jpg)
“METHOD”in Kim et al. 2001 paper(Phylogeny of Magnoliaceae)
![Page 41: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/41.jpg)
“METHOD”In Kim et al. 2001 paper(Phylogeny of Magnoliaceae)
http://amborella.net/2010MolecularPhylogeny/23-Kimetal2001AJBMagnoliaceae.pdf
![Page 42: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/42.jpg)
![Page 43: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/43.jpg)
Dandy (1927, 1950, 1978)and Hutchinson (1959)
Family Magnoliaceae
Tribe Magnolieae
Genus Magnolia L. (1753)Subgenus Magnolia
Section MagnoliaSection GwillimiaSection LiriantheSection RytidospermumSection OyamaSection TheorhodonSection GynopodiumSection Maingola
Subgenus YulaniaSection YulaniaSection BuergeriaSection Tulipastrum
Genus Talauma Juss. (1789)
Genus Aromadendron Blume (1825)
Genus Kmeria Dandy (1927)Genus Alcimandra Dandy (1927)
Genus Manglietia Blume (1823)
Genus Pachylarnax Dandy (1927)
Genus Elmerrillia Dandy (1927)
Genus Michelia L.(1753)
Genus Tsoongiodendron Chun (1963)Genus Paramichelia Hu (1940)
Tribe LiriodendreaeGenus Liriodendron L. (1753)
Law (1984)
Family MagnoliaceaeSubfamily Magnolioideae
Tribe MagnolieaeSubtribe Magnoliinae
Genus Magnolia
Genus TalaumaGenus Dugandiodendron Lozano-C. (1975)
Genus Aromadendron
Genus Parakmeria Hu and Cheng (1951)Genus KmeriaGenus Alcimandra
Subtribe ManglietiinaeGenus ManglietiaGenus Manglietiastrum Law (1979)
Genus Pachylarnax
Tribe MichelieaeSubtribe Elmerrilliinae
Genus ElmerrilliaSubtribe Micheliinae
Genus Michelia
Genus TsoongiodendronGenus Paramichelia
Subfamily LiriodendroideaeGenus Liriodendron
Nooteboom (1985)
Family MagnoliaceaeSubfamily Magnolioideae
Tribe Magnolieae
Genus MagnoliaSubgenus Magnolia
Section MagnoliaSection GwillimiaSection LiriantheSection RytidospermumSection OyamaSection TheorhodonSection GynopodiumSection MaingolaSection Alcimandra
Subgenus YulaniaSection YulaniaSection BuergeriaSection Tulipastrum
Subgenus TalaumaSection Talauma
Section BlumianaSection AromadendronSection Manglietiastrum
Genus Kmeria
Genus Manglietia
Genus Pachylarnax
Tribe Michelieae
Genus Elmerrillia
Genus Michelia
Subfamily LiriodendroideaeGenus Liriodendron
Chen and Nooteboom (1993)
Family MagnoliaceaeSubfamily Magnolioideae
Tribe Magnolieae
Genus MagnoliaSubgenus Magnolia
Section Gwillimia
Section RytidospermumSection Oyama
Section Gynopodium
Section AlcimandraSubgenus Yulania
Section YulaniaSection BuergeriaSection Tulipastrum
Subgenus Talauma
Section Blumiana
Genus Kmeria
Genus ManglietiaSection ManglietiaSection Manglietiastrum
Tribe Michelieae
Genus MicheliaSection MicheliaSection AnioschlamysSection DichlamysSection MicheliopsisSection TsoongiodendronSection Paramichelia
Subfamily LiriodendroideaeGenus Liriodendron
Law (1996)
Family Magnoliaceae
Tribe MagnolieaeSubtribe Manglietiinae
Genus MagnoliaSubgenus Magnolia
Section Gwillimia
Section RytidospermumSection OyamaSection Theorhodon
Subgenus YulaniaSection YulaniaSection BuergeriaSection Tulipastrum
Genus Talauma
Genus ParakmeriaGenus Kmeria
Subtribe ManglietiinaeGenus ManglietiaGenus Manglietiastrum
Subtribe AlcimandriinaeGenus Alcimandra
Subtribe Micheliinae
Genus MicheliaSection MicheliaSection AnisochlamysSection DichlamysSection Micheliopsis
Genus TsoongiodendronGenus Paramichelia
Genus LiriodendronTribe IllicieaeTribe Schisandreae
Fig. 2. Taxonomic treatments of the Magnoliaceae. Arrows indicate taxa whose taxonomic positions have been frequently changed. Gray boxes indicate species of the genus Magnolia by Nooteboom (1985). Chen and Nooteboom (1993) and Law (1996) treated only Chinese taxa including cultivated species in China.
![Page 44: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/44.jpg)
Chloroplast DNA regions analyzed in the study
0.5 1 kb0
LSC
SSC IRIR
trnK-2R
trnK 5
’exo
n
trnK 3
’exo
n
matK
trnK-3914F MK1 MK3 MK5 MK7 MK9
MK2R MK4R
1 MF298 972 MF1254MF1945
972RMF256R MF1861RMF1165R 2110R
MF561
MF1795
ndhF ORF 350
MF2095
1P14
ORF-2R
ndhFORF 350
IR MF1945MF1795
MF2095
ORF-R
2
Z1 647 1024
895R647R 1351R346R 3’
895
rbcL
3
50272R49855R
4987349317
trnL 5
’exo
n
trnL 3
’exo
n
trnF
5 6
7 8 94
AT1
RB
rbcL atpBATM
ATMR
PSAR
TRHF
trnH psbA
10
THMR
THM
Total sequenced base pairs:. 48 taxa X 8719 bp = 418,656 bp. 1/15 of total cpDNA
(excluding one IR region)
![Page 45: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/45.jpg)
Manglietia
Kmeria
Liriodendron
Pachylarnax
Elmerrillia
Michelia
Genus SubgenusSection
Magnolia
Magnolia
Magnolia
Magnolia
Yulania
Magnolia
Talauma
Magnolia
Magnolia
Talauma
Magnolia
Magnolia
Magnolia Magnolia
Talauma
Michelia
Maingola
AlcimandraYulania
BuergeriaBuergeriaBuergeria
Yulania
YulaniaYulaniaYulaniaYulaniaYulaniaBuergeriaTulipastrumBuergeriaTulipastrumTulipastrum
ManglietiastrumGynopodiumGynopodium
GwillimiaGwillimiaGwillimiaGwillimiaLiriantheBlumiana
GwillimiaRytidospermumRytidospermumRytidospermumRytidospermumOyamaOyamaOyamaOyama
TheorhodonTheorhodonTheorhodon
Magnolia
Theorhodon
Talauma
Rytidospermum
RytidospermumRytidospermumRytidospermum
MaingolaMaingola
Gynopodium
TheorhodonTheorhodonTheorhodonTheorhodon
TheorhodonTheorhodonTalauma
Talauma
Rytidospermum
Theorhodon
Blumiana
Magnolia
M. amoenaM. zenii
M. biondiiM. kobus
M. stellataM. dawsonianaM. sargentianaM. campbelliiM. sprengeri
M. denudataM. cylindricaM. liliiflora
M. salicifoliaM. acuminata var. acuminata
M. acu. var. subcordata
M. nitida var. lotungensisM. sinicaP. praecalva
M. nitida var. nitidaM. kachirachirai
Mang. duclouxiiMang. szechuanica
Mang. grandisMang. hebecarpa
Mang. aromaticaMang. conifera
Mang. insignisMang. dolichogyna
Mang. fordianaMang. glauca
Mang. megaphyllaMang. moto
M. panamensisM. poasana
M. iltisianaM. pacifica subsp. tarahumara
M. championiiM. coco
M. albosericeaM. henryi
M. pterocarpaM. liliifera M. gigantifolia
M. delavayiM. obovata
M. officinalisM. tripetala
M. rostrataM. sieboldii subsp. sinensisM. sieboldii subsp. sieboldii
M. wilsoniiM. globosa
M. portoricensisM. splendens
M. lenticellatumM. mahechaeM. mexicana
M. dodecapetalaM. fraseri var. fraseriM. fraseri var. pyramidata
K. duperreanaK. septentrionalis
M. macrophylla subsp. macrophyllaM. macrophylla subsp. ashei
M. dealbataL. chinensisL. tulipifera
32100 d31
139 d1
268 d2
267 d1
178 d1
163 d1
5
22
6100 d6
164 d11
1
162 d1
27
100 d61
599 d5
164 d1
164 d1 1
16
492 d4
164 d1
154 d1
165 d1
11
63 d12
21
1
277 d2
156 d1
53
287 d2 1
M. virginiana1
M. schedianaM. guatemalensisM. grandiflora
M. sharpii
M. tamaulipana
1
380 d3
161 d1
282 d2
1
52
111
5
266 d2
162 d1
163 d1
286 d2 1
11
271 d2
395 d34
3
147 d1
383 d3
492 d2 1
3
150 d1
11
64
98 d4119
100 d97
100 d6
162 d1
1
88
A
B
I
II
III
IV
V
VI
VII
Mich. cavalerieiMich. forveolataMich. macclureiMich. maudiaeMich. chapensisMich. martiniiMich. balanseM. pealiana
M. grifithiiM. gustaviiMich. champacaMich. lacei
Mich. masticataMich. montana
Mich. velutinaMich. baillonii
Mich. shiluensisMich. odora
Mich. wilsoniiMich. figoMich. doltsopaMich. hypolampra
Mich. floribundaE. ovalis
M. elegans
281 d2
158 d1
153 d1
162 d1
1
144 d1
12
42
160 d1
165 d1
166 d1
11
152 d1
22
15
Ia
Ib
Ic
Talauma
139 d1 1
Michelia
Michelia
Dichlamys
Michelia
Michelia
DichlamysDichlamys
Michelia
Michelia
Michelia
Tsoongiodendron
MicheliopsisAnisochylamys
Michelia
Michelia
Michelia
Michelia
Michelia
Michelia
Paramichelia
M. cathcartii3Talauma Aromadendr
on1
62 d1
Maximum parsimony tree
![Page 46: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/46.jpg)
Fig. 7. The neighbor-joining tree based on the ndhF sequences of the Magnoliaceae. Bootstrap values above 50% are shown above the branches.
M. nitida var. lotungensis
M. gustaviiMich. montana
Mich. champacaMich. baillonii
M. grifithiiMich. velutina
Mich. laceiMich. cavaleriei
Mich. forveolataMich. macclureiMich. maudiaeMich. chapensisMich. martiniiMich. masticata
M. pealianaMich. balanse
Mich. doltsopaMich. floribunda
Mich. hypolampraMich. shiluensisMich. odora
Mich. wilsoniiMich. figo
E. ovalisM. elegans
M. cathcartii
P. praecalva M. sinica
M. kachirachirai
M. amoenaM. kobusM. biondii
M. stellataM. zeniiM. denudataM. cylindricaM. liliiflora
M. salicifoliaM. campbelliiM. sprengeriM. dawsonianaM. sargentiana
M. acuminata var. acuminataM. acu. var. subcordata
M. obovataM. officinalis
M. tripetalaM. rostrata
M. globosaM. sieboldii subsp. sinensisM. sieboldii subsp. sieboldii
M. wilsoniiM. portoricensis
M. splendensM. lenticellatum
M. mahechaeM. mexicana
M. dodecapetalaM. fraseri var. fraseriM. fraseri var. pyramidata
K. duperreanaK. septentrionalis
M. gigantifoliaM. liliifera
M. championiiM. cocoM. henryi
M. albosericeaM. pterocarpa
M. delavayiM. iltisiana
M. pacifica subsp. tarahumaraM. sharpii
M. grandifloraM. schediana
M. panamensisM. poasana
M. guatemalensisM. tamaulipana
M. virginianaMang. duclouxii
Mang. szechuanicaMang. grandisMang. hebecarpa
Mang. coniferaMang. aromatica
Mang. insignisMang. dolichogyna
Mang. fordianaMang. megaphylla
Mang. glaucaMang. moto
M. macrophylla subsp. macrophyllaM. macrophylla subsp. asheiM. dealbata
L. chinensisL. tulipifera
0.0005 changes
Liriodendron
Elmerrillia
Michelia
Genus Subgenus Section
Magnolia
Magnolia
Manglietia
Magnolia
Yulania
Magnolia
Talauma
Magnolia
Magnolia
Talauma
Michelia
Michelia
Magnolia
Talauma
Magnolia
Magnolia
Magnolia
Magnolia
MaingolaMicheliaMicheliaParamicheliaMaingolaMicheliaMicheliaMicheliaMicheliaMicheliaMicheliaDichlamysDichlamysMicheliaMaingolaDichlamysMicheliaMicheliaAnisochlamysMicheliaTsoongiodendronMicheliaMicheliopsisAromadendronAlcimandra
ManglietiastrumGynopodiumGynopodiumGynopodium
YulaniaBuergeriaBuergeriaBuergeriaYulaniaYulaniaBuergeriaTulipastrumBuergeriaYulaniaYulaniaYulaniaYulaniaTulipastrumTulipastrum
RytidospermumRytidospermumRytidospermumRytidospermumOyamaOyamaOyamaOyamaTheorhodon Theorhodon TalaumaTalaumaTalaumaTalaumaRytidospermumRytidospermum
BlumianaBlumianaGwillimiaGwillimiaGwillimiaGwillimiaLiriantheGwillimiaTheorhodonTheorhodonTheorhodonTheorhodonTheorhodonTheorhodonTheorhodonTheorhodonTheorhodonMagnolia
RytidospermumRytidospermumRytidospermum
Magnolia Magnolia
Pachylarnax
Kmeria
Magnolia Magnolia
70100
61
54
57
6865
63
83
76
55
64
6178
90
67
100
61
83
64
100
99
6170
66
926164
5850
9974
9777
7751
99
100
87
5475
85
51
68
65506466
5857
87
100
62A
B
I
II
III
IV
V
VI
VII
Ia
Ib
Ic
Talauma
M. sinica M. nitida var. nitida
Neighbor-joining tree(Kimura’s two-parameter model)
![Page 47: Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular Phylogenetics/009-Chap.6.pdf · - Basic process to reconstruct phylogenetic tree Sequencing search](https://reader031.vdocuments.site/reader031/viewer/2022022009/5af3958d7f8b9a95468cc4fb/html5/thumbnails/47.jpg)
Phylogeny of Magnoliaceaebased on 10 chloroplast regions
Outgroup: Subfam. Liriodendroideae
MP tree
PAUP
Bootstrap value, Decay value
Characterchanges