Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular...

Chap. 6Inferring Molecular Phylogeny

- 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

Distances vs. Discrete characters

An example for comparing Character-based Method and Distance-based Method

“Phenetics vs. Phylogenetics” in Rordford et al.

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

c.f.) HTU: Hypothetical Taxonomic Unit

3) Set HTU1 and find minimum distanced taxa from HTU1

4) Reconstruct character status of HTU1 and add HTU1 in the matrix and distance table

5) Set HTU2 and find minimum distanced taxa again and repeat 3)~4).

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:

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

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.

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)

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

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

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

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

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


A

B

C

D

I

A

C

B

D

II

A

D

C

B

III

10 changes

11 changes

11 changes

Distance based method (phenetics)

B C

5

1.5

A

0.33

D


A

B

C

D

B A C D

B

C

D

A

1 step

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

Distances vs. Discrete characters

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

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

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

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

3) Heuristic search II

Star decomposition- Make a star tree first- Make several different nodes- Choose minimum stepped tree- Make different nodes…

In the heuristic search, we should repeat the analyses several times with different starting point to find “different tree islands”.

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.

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%

Remember! Consensus Tree- Strict consensus tree- semistrict consensus tree- 50% majority rule consensus tree

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

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

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

Long-branch attraction is always a problem in the phylogenetic analyses!

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

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.

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

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

Who can minimize long-branch attraction?

http://www.youtube.com/watch?v=H6IrUUDboZo

• Tree of Life Project(ToL): http://tolweb.org/tree/• KToL: Korean Tree of Life

“METHOD”in Kim et al. 2001 paper(Phylogeny of Magnoliaceae)

“METHOD”In Kim et al. 2001 paper(Phylogeny of Magnoliaceae)

http://amborella.net/2010MolecularPhylogeny/23-Kimetal2001AJBMagnoliaceae.pdf

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)


Tribe Magnolieae

Genus MagnoliaSubgenus Magnolia

Section MagnoliaSection GwillimiaSection LiriantheSection RytidospermumSection OyamaSection TheorhodonSection GynopodiumSection MaingolaSection Alcimandra


Subgenus TalaumaSection Talauma

Section BlumianaSection AromadendronSection Manglietiastrum

Genus Kmeria

Genus Manglietia

Genus Pachylarnax

Tribe Michelieae

Genus Elmerrillia

Genus Michelia


Chen and Nooteboom (1993)


Tribe Magnolieae


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


Law (1996)

Family Magnoliaceae

Tribe MagnolieaeSubtribe Manglietiinae


Section Gwillimia

Section RytidospermumSection OyamaSection Theorhodon


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.

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)

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

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)

Phylogeny of Magnoliaceaebased on 10 chloroplast regions

Outgroup: Subfam. Liriodendroideae

MP tree

PAUP

Bootstrap value, Decay value

Characterchanges

Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular...

Documents

Transcript of Chap. 6 Inferring Molecular Phylogeny - amborella.netamborella.net/2014-Molecular...