Phylogenomics
Jer-Ming Hu
胡哲明
Plant Systematics and Evolution Group, NTU
台大植物系統分類與演化研究室
本著作除另有註明外，採取創用CC「姓名標示－
非商業性－相同方式分享」台灣3.0版授權釋出
Unless noted, the course materials are licensed under Creative Commons
Attribution-NonCommercial-ShareAlike 3.0 Taiwan (CC BY-NC-SA 3.0)
1









14.4. Tue Introduction to models (Jarno)
16.4. Thu Distance-based methods (Jarno)
17.4. Fri ML analyses (Jarno)
20.4. Mon Assessing hypotheses (Jarno)
21.4. Tue Problems with molecular data (Jarno)
23.4. Thu Problems with molecular data
(Jarno)
Phylogenomics
24.4. Fri
Search algorithms, visualization, and
other computational aspects (Jarno)
J
Phylogenomics

The uses of phylogenetic principles to make sense of genomic data
 Recent reviews

Eisen, J.A. 1998. Gen. Res. 8: 163-167

Delsuc, F. et al. 2005. Nat. Rev. Genet. 6: 361-375

Koonin, E.V. 2005. Annu. Rev. Genet. 39: 309-338

Philippe, H. et al. 2005. Annu. Rev. Ecol. Evol. Syst. 36: 541-562

Boussau & Daubin (2010) TREE 25: 224-232
3
Current approaches
Methods based on primary sequences
Supermatrix
Supertree
Large-scale screening (e.g. ngs data)
Methods based on whole-genome features
Gene content
Gene order
DNA strings (distribution of oligonucleotides in genomes)
4
Combining data in phylogenetic analysis
Data partition
Different genes
Coding vs. non-coding regions
Among codon positions
Molecular vs. morphological data
Three ways to deal with partitioned data
Always combine (total evidence)
Never combine (separate analysis)
Conditional combine (perform a test to decide whether or not to
combine them)
Huelsenbeck, J.P. et al. (1996) TREE 11:152
5
Separate analysis
Miyamoto and Fitch (1995)
Tree should be estimated from each partition
Congruence among different data partitions provides stronger
evidence of accurate phylogeny
Miyamoto, M.M. and W.M. Fitch (1995) Syst. Biol. 44:64-76
6
Logic of total evidence
All independent characters should be included without a priori
consideration of data partition
Not only character data, but also taxa (e.g. fossil and living) should
be included in a phylogenetic analysis.
7
Conditional data combination
Bull et al. (1993), de Queiroz (1993)
The partitions should be subjected to a homogeneity test before any
further process.
e.g. KH test, partition homogeneity test, likelihood heterogeneity test,
etc.
Potential problem with false positives
The failure to combine data sets that should have been combined
Bull, J.J. et al. (1993) Syst. Biol. 42:384-397
de Queiroz, A. (1993) Syst. Biol. 42:368-372
8
Three ways for treating diverse data
Data 1
Data 2
Data 3
….
1
Test for homogeneity
Accept
Reject
2
3
Combined data
Separated data
National Taiwan University Jer-Ming Hu
9
The challenge of constructing large phylogenetic trees
Data availability matrix
Based on 130304 sequences of 14667 green plant species
Most GenBank sequences are from commonly
used genes and the model species
M. J. Sanderson and A. C. Driskell
10
Construct large phylogenies
M. J. Sanderson and A. C. Driskell
11
Problems of data concatenation
Including multiple genes may mix phylogenetic signals from
different evolutionary histories
Some sequences are usually unavailable for some species and have
to code them as missing data
e.g. photosynthetic genes of non-photosynthetic plants
12
Supertree approach: the idea
Past: (direct method) Nested source trees were
grafted together
O. R. P. Bininda-Emonds
Present: (indirect method) Overlapping source
trees are combined to yield to supertree
O. R. P. Bininda-Emonds
13
Supertree: constructing strict supertree
Source trees
A
D
E
F
B
C
Strict supertree A
A
B
C
D
E
Strict supertree B
D
E
F
A
National Taiwan University Jer-Ming Hu
B
C
D
E
F
14
Supertree by supermatrix approach
1. Combination of source data sets
2. Make a new tree
M. J. Sanderson, A. Purvis, and C. Henze
Sanderson. et al. (1998) TREE 13:105-109
15
Strict supertree algorithm
1. Identify common taxa
2. Construct a backbone tree
3. Examine source tree corresponding to
each branch
4. Strict consensus supertree
M. J. Sanderson, A. Purvis, and C. Henze
16
Supertree by MRP
Matrix Representation with Parsimony (MRP)
Remake a new data matrix which characters refer to the topologies
of the source trees
Baum, B.R. (1992) Taxon 41:3-10
Ragan, M.A. (1992) Mol. Phylo. Evol. 1:53-58
Sanderson. et al. (1998) TREE 13:105-109
17
Supertree by MRP
Source trees
1: present in the clade
0: absent in the clade
O. R. P. Bininda-Emonds, J. L. Gittleman, and M. A. Steel
18
BUILD algorithm
Aho et al. (1981) SIAM J. Comput. 10:405-421
Cluster C = X
4
3
2
1
4
6
5
1
National Taiwan University Jer-Ming Hu
C1 = {{1, 2}
{1, 2, 3}
{1, 2, 3, 4}}
C2 = {{1, 5}
{1, 5, 6}
{1, 5, 6, 4}}
19
BUILD algorithm
C’ = {{1,2,3,5,6}, {4}}
O. R. P. Bininda-Emonds, J. L. Gittleman, and M. A. Steel
Repeatedly evaluating the clusters
C’’ = {{1,2,5}, {3}, {6}}
C = {{1,2,3,4,5,6}, {1,2,3,5,6}, {1,2,5}, {3},
{4}, {6}}
O. R. P. Bininda-Emonds, J. L. Gittleman, and M. A. Steel
20
Two source trees
4
3
2
4 6 3 5
2
1
4
1
The BUILD tree
6
5
4 6 3 5
1
2
1
The MRP tree
National Taiwan University Jer-Ming Hu
21
Current supertree methods
O. R. P. Bininda-Emonds
Bininda-Emonds, O.R.P. (2004) TREE 19.315
22
O. R. P. Bininda-Emonds
23
Supertree: the future
A divide-and-conquer approach can be applied, to decompose very
large phylogenetic problem into many smaller subproblems, and the
solutions to which are combined to derive the global answer
Similar approaches have been used in phylogenetics, e.g.
compartmentalization and quartet puzzling
Two new approaches
•
•
Disk-covering methods (DCMs)
The biclique method
Bininda-Emonds, O.R.P. (2004) TREE 19.315
24
Disk-covering method (DCM)
O. R. P. Bininda-Emonds
25
The biclique method
O. R. P. Bininda-Emonds
26
Critics of supertree approach

It does not take sequence info into account

The dataset is non-independent

MRP favors larger source trees because they contribute more
characters

Some direct methods cannot incorporate support values into the
source trees
27
Programs available
supertree
Rod Page
http://darwin.zoology.gla.ac.uk/~rpage/supertree/
SuperTree
Salamin et al. (2002)
http://www2.unil.ch/phylo/bioinformatics/supertree.html
Supertrees related
Olaf R.P. Bininda-Emonds
http://www.molekularesystematik.uni-oldenburg.de/en/34011.html
28
... okay, let’s see some real data
Supertree of legumes related to Astragalus
Sanderson, M.J. et al. (1998) TREE 13:105-109
Supertree of prokaryotes
Daubin, V. et al. (2002) Genome Res. 12:1080
Supertree of the angiosperms
Davies, T.J. et al. (2004) PNAS 101:1904-1909
29
M. J. Sanderson, A. Purvis, and C. Henze
Bold faces: taxa in common
M. J. Sanderson, A. Purvis, and C. Henze
M. J. Sanderson, A. Purvis, and C. Henze
30
Genome Research (2002) 12:1080-1090
A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes
Sharing a Common History
Vincent Daubin, Manolo Gouy, and Guy Perriere
Supertree using MRP
• 730 source trees, include 45 taxa
• Bootstrap % used as character weights
• BIONJ + gamma
• Identify the core of genes
• Principal Coordinates analysis (PCO) for comparing tree distance
(Robinson-Foulds distance)
•
V. Daubin, M. Gouy, and G. Perriere
31
Supertree made w/ ML trees
Chlamydiales
Spirochaetes
Hyperthermophilic bacteria
Cyanobacteria
Low GC Gram+
Deinococcus
High GC Gram+
Proteobacteria
Crenarchaeota
Euryarchaeota
Eukaryota
V. Daubin, M. Gouy, and G. Perriere
Supertree constructed from 730 gene trees
32
Supertree approach
Plot of the first two axes of the PCO (Principle Coordinate Analysis)
Identifying “core genes”
Choose only the “core genes &
perform supertree searching
again
V. Daubin, M. Gouy, and G. Perriere
33
Supertree made w/ ML trees after PCO
Spirochaetes
Chlamydiales
Hyperthermophilic bacteria
Low GC Gram+
Cyanobacteria
Deinococcus
High GC Gram+
Proteobacteria
Euryarchaeota
Crenarchaeota
Eukaryota
V. Daubin, M. Gouy, and G. Perriere
34
PNAS (2004) 101:1904-1909
Darwin's abominable mystery: Insights from a supertree of the
angiosperms
T. Johathan Davies, Timothy G. Barraclough, Mark W. Chase, Pamela S. Soltis, Douglas E. Soltis, and Vincent Savolainen
Supertree using MRP
• 46 source trees, include 379 taxa
• Bootstrap % used as character weights
• Examining diversification rates
•
V. T. J. Davies, T. G. Barraclough, M. W. Chase, P. S. Soltis, D. E. Soltis, and V. Savolainen
35
PNAS (2004) 101:1904-1909
Darwin's abominable mystery: Insights from a supertree of the
angiosperms
T. Johathan Davies, Timothy G. Barraclough, Mark W. Chase, Pamela S. Soltis, Douglas E. Soltis, and Vincent Savolainen
Supporting Table 2
36
1 of 10000 most parsimonious supertrees with
dates obtained by NPRS of ML using rbcL
Diversification rates
Low
Low - medium
Medium - high
High
Time calibrated by 84 mya of Fagales/Cucurbitales split
V. T. J. Davies, T. G. Barraclough, M. W. Chase, P. S. Soltis, D. E. Soltis, and V. Savolainen
37
V. T. J. Davies, T. G. Barraclough, M. W. Chase, P. S. Soltis, D. E. Soltis, and V. Savolainen
No ‘key innovations’ can be identified
38
Phylogenomics using whole-genome features
Distribution of sequence strings
Transformation of the frequencies of small oligonucleotides (up to
eight) or oligopeptides (up to six) into distances and used for
phylogenetic reconstruction
Gene order methods
Gene content methods
39
Genome sequences
Analyzed the tetranucleotide
usage deviations from
expectations (TUD)
AAAA
AAAC
AAAG
AAAT
...
CAAA
CAAC
...
TTTT
Compare among different
genomes
Use the similarity measures to
construct a distance based phylogeny
National Taiwan University Jer-Ming Hu
40
Potential problems using sequence strings
The phylogeneic information of sequence strings saturates rapidly
No models of evolution is proposed for such distribution of
oligonucleotide or oligopeptide frequencies
41
16S rRNA tree
TUD tree
D. T. Pride, R. J. Meinersmann, T. M. Wassenaar, and M. J. Blaser
Gram-negative
Gram-positive
Archaea and thermophilic bacteria
Gram-negative
42
Gene order method
Information of genome organization
Distances of two genomes can be computed to minimize the
numbers of inversions, transpositions, insertions, and deletions
Distances can also be computed for the minimum number of pairs of
genes next to each other in one of the two genomes, but not in the
other (“break-point distance”)
43
Distribution of conserved gene pairs among 31 clades of
prokaryotes
Wolf et al. (2001) BMC Evol. Biol. 1:8
Y. I. Wolf, I. B. Rogozin, N. V. Grishin, R. L. Tatusov, E. V. Koonin
Gene-order phylogeny
ss rRNA phylogeny
J. O. Korbel, B. Snel, M. A. Huynen, and P. Bork J. O. Korbel, B. Snel, M. A. Huynen, and P. Bork
44
Gene content method
Construct distance or parsimony phylogeny based on the proportion
of shared orthologous genes between genomes
A data matrix is made for the presence/absence of orthologous genes
•
Note: universal present genes will become parsimonious uninformative!
45
Example of comparing gene contents
B. Snel, P. Bork, M. A. Huynen
1. Large genomes have many genes in common
2. The number of genes two genomes have in common depends on their evolutionary
distance
46
Gene-content phylogeny
ss rRNA phylogeny
J. O. Korbel, B. Snel, M. A. Huynen, and P. Bork
J. O. Korbel, B. Snel, M. A. Huynen, and P. Bork
Note that proteobacteria in gene-content phylogeny is not
monophyletic
47
Problems using gene-content method
Big/small genome attraction
Artificial grouping of unrelated species with small genomes, e.g.
Mycoplasma, Buchnera, Chlamydia, or Rickettsia.
Phylogenetic positions of some taxa do not agree with previous
studies
Halobacterium never clusters with Methanosarcina. This is probably
due to too many HGTs
48
Programs available
SHOT
A web server for the construction of genome phylogenies
http://coot.embl.de/~korbel/SHOT/
49
Summary
R. Delsuc, H. Brinkmann, and H. Philippe
50
Large scale screening of orthologous genes for
phylogenomic analysis
G. D. Edgecombe, G. Giribet, C. W. Dunn, A.
Hejnol, R. M. Kristensen, R. C. Neves, G. W.
Rouse, K. Worsaae, and M. V. Sørensen
This work is licensed by SpringerLink for the use of “Course Database of General Education TW” ONLY.
The copyright belongs to the above mentioned entity and GET does not have the authorization right.
Copyright privileges have to be negotiated with the copyright owner(s) for separately.
G. D. Edgecombe, G. Giribet, C. W. Dunn, A.
Hejnol, R. M. Kristensen, R. C. Neves, G. W.
Rouse, K. Worsaae, and M. V. Sørensen
This work is licensed by SpringerLink for the use of “Course Database of General Education TW” ONLY. The copyright belongs to the above mentioned
entity and GET does not have the authorization right. Copyright privileges have to be negotiated with the copyright owner(s) for separately.
51
Flow chart for EST-based phylogenomic analysis
C. W. Dunn, A. Hejnol, D. Q. Matus, K. Pang, W. E. Browne, S. A. Smith, E.
Seaver, G. W. Rouse, M. Obst, G. D. Edgecombe, M. V. Sørensen6, S. H. D.
Haddock, A. Schmidt-Rhaesa, A. Okusu, R. M. Kristensen, W. C. Wheeler, M. Q.
Martindale, and G. Giribet
52
Phylogeny based on 77
taxa, 150 genes, of the
animal tree of life
C. W. Dunn, A. Hejnol, D. Q. Matus, K. Pang, W. E. Browne, S.
A. Smith, E. Seaver, G. W. Rouse, M. Obst, G. D. Edgecombe,
M. V. Sørensen6, S. H. D. Haddock, A. Schmidt-Rhaesa, A.
Okusu, R. M. Kristensen, W. C. Wheeler, M. Q. Martindale, and
G. Giribet
Dunn et al. (2008) Nature 452: 745
53
The myth of orthologous gene families
Bastien Boussau, and Vincent Daubin
54
“Phylogenetic awareness” on making tree
Bastien Boussau, and Vincent Daubin
55
Problems of just using whole-genome data
Case study of seeking the root of angiosperms
Amborella or monocots?
Flickr scott.zona
Flickr adrien2008
56
Amborella
Flickr pennstatelive
Amborella as the first branch has been identified in 18S
rDNA, chl. atpB, phyA/C, mt coxI, matR, and combined
analysis
S. Stefanović, D. W. Rice, and J. D. Palmer
57
Phylogeny of monocots being basal according to complete chloroplast genomes
Eudicots
Monocots
V. V. Goremykin, K. I. Hirsch-Ernst, S. Wolfl, and F. H. Hellwig
58
•No rate categories
•1st/2nd pos only
•4 gamma rate categories
•1st/2nd pos only
•No rate categories
•Estimated proportion of
invariant sites
•1st/2nd pos only
•No rate categories
•all pos
S. Stefanović, D. W. Rice, and J. D. Palmer
59
Effects of taxon sampling
Method: DNA ML HKY85 with no rate categories
Sampling according to Goremykin
et al. (2004)
Acorus instead of grasses
Acorus and grasses included
S. Stefanović, D. W. Rice, and J. D. Palmer
Long Branch Attraction effect
60
Copyright Declaration
Work
Licensing
Author/Source
Page
P8
National Taiwan University Jer-Ming Hu
M. J. Sanderson and A. C. Driskell
2003. The challenge of constructing large
phylogenetic trees. Trends in Plant Science 8: p. 374.
http://www.sciencedirect.com/science/article/pii/S1360138503001651
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Elsevier Website Terms and Conditions
http://www.elsevier.com/wps/find/termsconditions.cws_home/termsconditions
P9
M. J. Sanderson and A. C. Driskell
2003. The challenge of constructing large
phylogenetic trees. Trends in Plant Science 8: p. 375.
http://www.sciencedirect.com/science/article/pii/S1360138503001651
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Elsevier Website Terms and Conditions
http://www.elsevier.com/wps/find/termsconditions.cws_home/termsconditions
P10
O. R. P. Bininda-Emonds
2004. The evolution of supertrees. Trends in Ecology & Evolution 19: p. 315.
http://www.sciencedirect.com/science/article/pii/S0169534704000709
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Elsevier Website Terms and Conditions
http://www.elsevier.com/wps/find/termsconditions.cws_home/termsconditions
P12
O. R. P. Bininda-Emonds
2004. The evolution of supertrees. Trends in Ecology & Evolution 19: p. 315.
http://www.sciencedirect.com/science/article/pii/S0169534704000709
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Elsevier Website Terms and Conditions
http://www.elsevier.com/wps/find/termsconditions.cws_home/termsconditions
P12
61
Work
Licensing
Author/Source
Page
P13
National Taiwan University Jer-Ming Hu
M. J. Sanderson, A. Purvis, and C. Henze
1998. Phylogenetic supertrees: Assembling the trees of life. Trends in Ecology & Evolution 13:
p. 106.
http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347%2897%2901242-1
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Cell Press Copyrights and Limitations on Use
•Elsevier Website Terms and Conditions
•The "Code of Best Practices in Fair Use for OpenCourseWare 2009
(http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A
Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section
107 of the 1976 U.S. Copyright Act
P14
M. J. Sanderson, A. Purvis, and C. Henze
1998. Phylogenetic supertrees: Assembling the trees of life. Trends in Ecology & Evolution 13:
p. 107.
http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347%2897%2901242-1
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Cell Press Copyrights and Limitations on Use
•Elsevier Website Terms and Conditions
•The "Code of Best Practices in Fair Use for OpenCourseWare 2009
(http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A
Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section
107 of the 1976 U.S. Copyright Act
P15
O. R. P. Bininda-Emonds, J. L. Gittleman, and M. A. Steel
2002. THE (SUPER)TREE OF LIFE: Procedures, Problems, and Prospects. Annual Review of
Ecology and Systematics 33: p. 268.
http://www.annualreviews.org/doi/pdf/10.1146/annurev.ecolsys.33.010802.150511
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Annual Reviews Copyright & Permissions
http://www.annualreviews.org/page/about/copyright-and-permissions
P17
62
Work
Licensing
Author/Source
Page
P18
National Taiwan University Jer-Ming Hu
O. R. P. Bininda-Emonds, J. L. Gittleman, and M. A. Steel
2002. THE (SUPER)TREE OF LIFE: Procedures, Problems, and Prospects. Annual Review of
Ecology and Systematics 33: p. 273.
http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.33.010802.150511?journalCo
de=ecolsys.1
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Annual Reviews Copyright & Permissions
http://www.annualreviews.org/page/about/copyright-and-permissions
P19
O. R. P. Bininda-Emonds, J. L. Gittleman, and M. A. Steel
2002. THE (SUPER)TREE OF LIFE: Procedures, Problems, and Prospects. Annual Review of
Ecology and Systematics 33: p. 273.
http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.33.010802.150511?journalCo
de=ecolsys.1
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Annual Reviews Copyright & Permissions
http://www.annualreviews.org/page/about/copyright-and-permissions
P19
P20
National Taiwan University Jer-Ming Hu
O. R. P. Bininda-Emonds
2004. The evolution of supertrees. Trends in Ecology & Evolution 19: p. 317.
http://www.sciencedirect.com/science/article/pii/S0169534704000709
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Elsevier Website Terms and Conditions
http://www.elsevier.com/wps/find/termsconditions.cws_home/termsconditions
P21
63
Work
Licensing
Author/Source
Page
O. R. P. Bininda-Emonds
2004. The evolution of supertrees. Trends in Ecology & Evolution 19: p. 318.
http://www.sciencedirect.com/science/article/pii/S0169534704000709
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Elsevier Website Terms and Conditions
http://www.elsevier.com/wps/find/termsconditions.cws_home/termsconditions
P22
O. R. P. Bininda-Emonds
2004. The evolution of supertrees. Trends in Ecology & Evolution 19: p. 320.
http://www.sciencedirect.com/science/article/pii/S0169534704000709
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Elsevier Website Terms and Conditions
http://www.elsevier.com/wps/find/termsconditions.cws_home/termsconditions
P24
O. R. P. Bininda-Emonds
2004. The evolution of supertrees. Trends in Ecology & Evolution 19: p. 320.
http://www.sciencedirect.com/science/article/pii/S0169534704000709
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Elsevier Website Terms and Conditions
http://www.elsevier.com/wps/find/termsconditions.cws_home/termsconditions
P25
M. J. Sanderson, A. Purvis, and C. Henze
1998. Phylogenetic supertrees: Assembling the trees of life. Trends in Ecology & Evolution 13:
p. 108.
http://download.cell.com/trends/ecology-evolution/pdf/PIIS0169534797012421.pdf
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Cell Press Copyrights and Limitations on Use
•Elsevier Website Terms and Conditions
•The "Code of Best Practices in Fair Use for OpenCourseWare 2009
(http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A
Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section
107 of the 1976 U.S. Copyright Act
P29
64
Work
Supertree using MRP
730 source trees, …
Principal Coordinates analysis
(PCO) for comparing tree distance
(Robinson-Foulds distance)
Licensing
Author/Source
Page
M. J. Sanderson, A. Purvis, and C. Henze
1998. Phylogenetic supertrees: Assembling the trees of life. Trends in Ecology & Evolution 13:
p. 108.
http://download.cell.com/trends/ecology-evolution/pdf/PIIS0169534797012421.pdf
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Cell Press Copyrights and Limitations on Use
•Elsevier Website Terms and Conditions
•The "Code of Best Practices in Fair Use for OpenCourseWare 2009
(http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A
Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section
107 of the 1976 U.S. Copyright Act
P29
M. J. Sanderson, A. Purvis, and C. Henze
1998. Phylogenetic supertrees: Assembling the trees of life. Trends in Ecology & Evolution 13:
p. 108.
http://download.cell.com/trends/ecology-evolution/pdf/PIIS0169534797012421.pdf
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Cell Press Copyrights and Limitations on Use
•Elsevier Website Terms and Conditions
•The "Code of Best Practices in Fair Use for OpenCourseWare 2009
(http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A
Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section
107 of the 1976 U.S. Copyright Act
P29
Vincent Daubin, Manolo Gouy, and Guy Perriere
A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a
Common History
http://genome.cshlp.org/content/12/7/1080.full
2012/06/14 visited
P30
V. Daubin, M. Gouy, and G. Perriere.
2002. A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes
Sharing a Common History. Genome Research 12: p. 1082.
Copyright © 2002, by Cold Spring Harbor Laboratory Press
http://genome.cshlp.org/content/12/7/1080.full.pdf+html
2012/06/14 visited
P31
V. Daubin, M. Gouy, and G. Perriere.
2002. A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes
Sharing a Common History. Genome Research 12: p. 1083.
Copyright © 2002, by Cold Spring Harbor Laboratory Press
http://genome.cshlp.org/content/12/7/1080.full.pdf+html
2012/06/14 visited
P32
65
Work
Supertree using MRP
46 source trees, include 379 taxa
Bootstrap % used as character
weights
Examining diversification rates
Licensing
Author/Source
Page
V. Daubin, M. Gouy, and G. Perriere.
2002. A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes
Sharing a Common History. Genome Research 12: p. 1084.
Copyright © 2002, by Cold Spring Harbor Laboratory Press
http://genome.cshlp.org/content/12/7/1080.full.pdf
2012/06/14 visited
P33
V. T. J. Davies, T. G. Barraclough, M. W. Chase, P. S. Soltis, D. E. Soltis, and V. Savolainen
2004. Darwin's abominable mystery: Insights from a supertree of the angiosperms. PNAS 101:
p. 1904-1909.
http://www.pnas.org/content/101/7/1904.full.pdf+html
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•The National Academies Terms of Use
•The "Code of Best Practices in Fair Use for OpenCourseWare 2009
(http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A
Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section
107 of the 1976 U.S. Copyright Act
P34
V. T. J. Davies, T. G. Barraclough, M. W. Chase, P. S. Soltis, D. E. Soltis, and V. Savolainen
2004. Darwin's abominable mystery: Insights from a supertree of the angiosperms. PNAS 101:
p. 1906.
http://www.pnas.org/content/101/7/1904.full.pdf+html
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•The National Academies Terms of Use
•The "Code of Best Practices in Fair Use for OpenCourseWare 2009
(http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A
Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section
107 of the 1976 U.S. Copyright Act
P36
V. T. J. Davies, T. G. Barraclough, M. W. Chase, P. S. Soltis, D. E. Soltis, and V. Savolainen
2004. Darwin's abominable mystery: Insights from a supertree of the angiosperms. PNAS 101:
p. 1908.
http://www.pnas.org/content/101/7/1904.full.pdf+html
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•The National Academies Terms of Use
•The "Code of Best Practices in Fair Use for OpenCourseWare 2009
(http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A
Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section
107 of the 1976 U.S. Copyright Act
P37
P39
National Taiwan University Jer-Ming Hu
66
Work
Licensing
Author/Source
Page
D. T. Pride, R. J. Meinersmann, T. M. Wassenaar, and M. J. Blaser
2003. Evolutionary Implications of Microbial Genome Tetranucleotide Frequency Biases.
Genome Research 13: p. 152.
http://genome.cshlp.org/content/13/2/145.full.pdf+html
2012/06/14 visited
P41
D. T. Pride, R. J. Meinersmann, T. M. Wassenaar, and M. J. Blaser
2001. Genome trees constructed using five different approaches suggest new major bacterial
clades. BMC Evolutionary Biology 1: 8.
http://www.biomedcentral.com/content/pdf/1471-2148-1-8.pdf
2012/06/14 visited
P43
J. O. Korbel, B. Snel, M. A. Huynen, and P. Bork
2002. SHOT: a web server for the construction of genome phylogenies. Trends in Genetics 18:
p. 160.
http://www.cell.com/trends/genetics/abstract/S0168-9525%2801%2902597-5
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Cell Press Copyrights and Limitations on Use
•Elsevier Website Terms and Conditions
•The "Code of Best Practices in Fair Use for OpenCourseWare 2009
(http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A
Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section
107 of the 1976 U.S. Copyright Act
P43
J. O. Korbel, B. Snel, M. A. Huynen, and P. Bork
2002. SHOT: a web server for the construction of genome phylogenies. Trends in Genetics 18:
p. 161.
http://www.cell.com/trends/genetics/abstract/S0168-9525%2801%2902597-5
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Cell Press Copyrights and Limitations on Use
•Elsevier Website Terms and Conditions
•The "Code of Best Practices in Fair Use for OpenCourseWare 2009
(http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A
Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section
107 of the 1976 U.S. Copyright Act
P43, P46
67
Work
Licensing
Author/Source
Page
B. Snel, P. Bork, M. A. Huynen
1999. Genome phylogeny based on gene content, Nature Genetics 21: p. 108.
http://www.nature.com/ng/journal/v21/n1/pdf/ng0199_108.pdf
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Nature Terms and Conditions
P45
J. O. Korbel, B. Snel, M. A. Huynen, and P. Bork
2002. SHOT: a web server for the construction of genome phylogenies. Trends in Genetics 18:
p. 159.
http://www.cell.com/trends/genetics/pdf/PIIS0168952501025975.pdf
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Cell Press Copyrights and Limitations on Use
•Elsevier Website Terms and Conditions
•The "Code of Best Practices in Fair Use for OpenCourseWare 2009
(http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A
Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section
107 of the 1976 U.S. Copyright Act
P46
R. Delsuc, H. Brinkmann, and H. Philippe
2005. Phylogenomics and the reconstruction of the tree of life. Nature Reviews Genetics 6: p.
363.
http://www.nature.com/nrg/journal/v6/n5/pdf/nrg1603.pdf
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Nature Terms and Conditions
P49
G. D. Edgecombe, G. Giribet, C. W. Dunn, A. Hejnol, R. M. Kristensen, R. C. Neves, G. W.
Rouse, K. Worsaae, and M. V. Sørensen
Organisms Diversity & Evolution 11: p. 155.
http://www.springerlink.com/content/5608113750q30314/fulltext.pdf?MUD=MP
This work is licensed by SpringerLink for the use of “Course Database of General Education
TW” ONLY. The copyright belongs to the above mentioned entity and GET does not have the
authorization right. Copyright privileges have to be negotiated with the copyright owner(s)
for separately.
P50
68
Work
Licensing
Author/Source
Page
G. D. Edgecombe, G. Giribet, C. W. Dunn, A. Hejnol, R. M. Kristensen, R. C. Neves, G. W.
Rouse, K. Worsaae, and M. V. Sørensen
Organisms Diversity & Evolution 11: p. 155.
http://www.springerlink.com/content/5608113750q30314/fulltext.pdf?MUD=MP
This work is licensed by SpringerLink for the use of “Course Database of General Education
TW” ONLY. The copyright belongs to the above mentioned entity and GET does not have the
authorization right. Copyright privileges have to be negotiated with the copyright owner(s)
for separately.
P50
C. W. Dunn, A. Hejnol, D. Q. Matus, K. Pang, W. E. Browne, S. A. Smith, E. Seaver, G. W.
Rouse, M. Obst, G. D. Edgecombe, M. V. Sørensen6, S. H. D. Haddock, A. Schmidt-Rhaesa,
A. Okusu, R. M. Kristensen, W. C. Wheeler, M. Q. Martindale, and G. Giribet
2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature
452: p. 745-349
http://www.nature.com/nature/journal/v452/n7188/extref/nature06614-s1.pdf
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Nature Terms and Conditions
P51
C. W. Dunn, A. Hejnol, D. Q. Matus, K. Pang, W. E. Browne, S. A. Smith, E. Seaver, G. W.
Rouse, M. Obst, G. D. Edgecombe, M. V. Sørensen6, S. H. D. Haddock, A. Schmidt-Rhaesa,
A. Okusu, R. M. Kristensen, W. C. Wheeler, M. Q. Martindale, and G. Giribet
2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature
452: p. 746.
http://www.nature.com/nature/journal/v452/n7188/full/nature06614.html?free=2
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Nature Terms and Conditions
P52
Bastien Boussau, and Vincent Daubin
2010. Genomes as documents of evolutionary history. Trends in Ecology & Evolution 25: p.
228.
http://www.sciencedirect.com/science/article/pii/S0169534709002973
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Elsevier Website Terms and Conditions
http://www.elsevier.com/wps/find/termsconditions.cws_home/termsconditions
P53
69
Work
Licensing
Author/Source
Page
Bastien Boussau, and Vincent Daubin
2010. Genomes as documents of evolutionary history. Trends in Ecology & Evolution 25: p.
225.
http://www.sciencedirect.com/science/article/pii/S0169534709002973
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Elsevier Website Terms and Conditions
http://www.elsevier.com/wps/find/termsconditions.cws_home/termsconditions
P54
P55
Flickr scott.zona
http://www.flickr.com/photos/scottzona/3173820625/sizes/l/in/photostream/
2012/06/14 visited
P55
Flickr adrien2008
http://www.flickr.com/photos/adrien2008/4647588299/sizes/l/in/photostream/
2012/06/14 visited
P56
S. Stefanović, D. W. Rice, and J. D. Palmer
2004. Long branch attraction, taxon sampling, and the earliest
angiosperms: Amborella or monocots? BMC Evolutionary Biology 4: 35.
http://w01.biomedcentral.com/content/pdf/1471-2148-4-35.pdf
2012/06/14 visited
P56
Flickr pennstatelive
http://www.flickr.com/photos/pennstatelive/5609235215/sizes/l/in/photostream/
2012/06/14 visited
70
Work
Licensing
Author/Source
Page
V. V. Goremykin, K. I. Hirsch-Ernst, S. Wolfl, and F. H. Hellwig
2004. The Chloroplast Genome of Nymphaea alba: Whole-Genome Analyses and the Problem
of Identifying the Most Basal Angiosperm. Molecular Biology and Evolution 21: p. 1448.
http://mbe.oxfordjournals.org/content/21/7/1445.full
It is used subject to the fair use doctrine of:
•Taiwan Copyright Act Articles 52 & 65
•Oxford Journals Terms & Conditions for Use
http://www.oxfordjournals.org/our_journals/terms.html
P57
S. Stefanović, D. W. Rice, and J. D. Palmer
2004. Long branch attraction, taxon sampling, and the earliest
angiosperms: Amborella or monocots? BMC Evolutionary Biology 4: 35.
http://w01.biomedcentral.com/1471-2148/4/35/
2012/06/14 visited
P58
S. Stefanović, D. W. Rice, and J. D. Palmer
2004. Long branch attraction, taxon sampling, and the earliest
angiosperms: Amborella or monocots? BMC Evolutionary Biology 4: 35.
http://w01.biomedcentral.com/1471-2148/4/35/
2012/06/14 visited
P59
71
Whales
retrotransposons
72
Four proposed whale phylogeny trees
http://www.pnas.org/content/98/13/7384.full
73
Whale phylogeny based on retrotransposon
http://www.pnas.org/content/98/13/7384.full
74
Synteny
chromosome level
75
Hands are chromosomes, each card is a gene
Deal 1
http://www.nature.com/scitable/topicpage/synteny-inferring-ancestral-
76
Hands are chromosomes, each card is a gene
Deal 2
http://www.nature.com/scitable/topicpage/synteny-inferring-ancestral-
77
Hands are chromosomes, each card is a gene
Deal 3: inversion
http://www.nature.com/scitable/topicpage/synteny-inferring-ancestral-
78
Hands are chromosomes, each card is a gene
Deal 4: reciprocal translocation
http://www.nature.com/scitable/topicpage/synteny-inferring-ancestral-
79
Ensembl Genome Browser
80
SYMAP example
81
Synteny in phylogenetics
•Full genome comparisons
•Not necessarily very simple algorithms
•Might no be feasible for large numbers of taxa
•http://www.ncbi.nlm.nih.gov/pmc/articles/PMC267598
2/
•Recode and use standard maximum likelihood
•http://psb.stanford.edu/psbonline/proceedings/psb13/lin.pdf
82
83