part 02 phylogenetics

8/3/2019 Part 02 Phylogenetics

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Principles of Phylogenetic Systematics

Grecebio Jonathan D. Alejandro, Ph.D.

Research Center for the Natural Sciences and College of Science , University of Santo Tomas,

Manila, 1008 Philippines. [email protected]
mailto:[email protected]:[email protected]


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Topic outline

Systematics & Phylogenetic Revolution

Phenetics vs Phylogenetics/Cladistics

Phylogenetic characters/terminologies

Phylogenetic trees & grouping (Parsimony)

Phylogenetic approaches

Sources of molecular data

Advantages of using molecular data

E.g., Application of phylogenetics usingmolecular data

Basic Methods in Phylogenetics


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Stuessy 1979:622



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Phylogenetic systematics- reconstruction and studyof evolutionary relationships.

Evolutionary theory similarity among species isdue to a common descent, or inheritance from a

common ancestor.

Phylogeny - the historical relationships amonglineages or organisms, such as their genes.

Willi Hennig(German entomologist, 1950s)proposed that systematics should reflect theknown evolutionary history of lineages asclosely as possible, an approach he calledphylogenetic systematics.
http://images.google.de/imgres?imgurl=http://www.cladistics.org/about/hennig2.jpg&imgrefurl=http://www.cladistics.org/about/hennig.html&h=201&w=181&sz=11&tbnid=9wzOIhFZqagJ:&tbnh=99&tbnw=89&hl=de&start=3&prev=/images%3Fq%3Dwilli%2Bhennig%26svnum%3D10%26hl%3Dde%26lr%3D%26sa%3DG


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The followers of Hennig were disparingly referred to

as"cladists"by his opponents, because of theemphasis on recognizing onlymonophyleticgroups, a group plus all of its descendents, orclades.However, the cladists quickly adopted thatterm as a helpful label, andnowadays, cladisticapproaches to systematics are used routinely.

Phylogenetics = Cladistics


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Phenetics vs Cladistics

characteristics identity

critter A 4 limbs meta.

kidney

hair endothermy viv ip. no

cloaca

placental

critter B 4 limbs meta.

kidney

hair endothermy ovip. cloaca echidna

critter C 4 limbs meta.

kidney

feathers endothermy ovip. cloaca bird

Phenetic (overall similarity)

A

B

Coverall similarity

C B A

3

4

5


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characteristics identity

critter A 4 limbs meta.

kidney

hair endothermy viv ip. no

cloaca

placental

critter B 4 limbs meta.

kidney

hair endothermy ovip. cloaca echidna

critter C 4 limbs meta.

kidney

feathers endothermy ovip. cloaca bird

ancestor 4 limbs meta.

kidney

no

hair/feathers

ectothermy ovip. cloaca turtle

Cladistics (character evolution; e.g. shared derived characters)

A

B

C

shared derived characters(synapomorphy)

A B C

1

2

1


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Characters

1 2 3 4 5

Species A 0 0 0 0 0B 1 1 0 0 0

C 1 0 1 1 1

Phenetic CladisticOverall similarities

A B C

A - .60 .20

B - .20

C -Similarity

%

100 A B C80

60

40

200

0 = Primitive character state

or plesiomorphic

1 = Derived character state

Character 1 = shared derived or

synapomorphic

Character 2 = uniquely derived or

autopomorphic

A B C

Character 1


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Phylogenetic trees

Cladogram


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Phylogenetic trees


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Phylogenetic trees


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Phylogenetic grouping

A monophyletic group includes the most recentcommon ancestor of the group and all of itsdescendants.


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A paraphyletic group includes the most recent

common ancestor of the group, but not all ofits descendants.


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A polyphyletic group does not include the most

recent common ancestor of all the members.

Pseudomussaenda stenocarpa

Sabicea diversifoliaWarszewiczia coccineaHeinsia crinitaHeinsia zanzibaricaHeinsia busseiLandiopsis capuroniiMussaenda sp. nov.Mussaenda pervilleiMussaenda latisepalaMussaenda erectiloba

Mussaenda vestitaPseudomussaenda rivularis

Pseudomussaenda flavaMussaenda arcuataMussaenda monticolaMussaenda niveaMussaenda erythrophyllaMussaenda elegansMussaenda grandifloraMussaenda isertianaMussaenda afzelii

Mussaenda pubescensMussaenda shikokianaMussaenda parvifoliaMussaenda unifloraMussaenda unifloraMussaenda unifloraMussaenda reinwardtianaMussaenda nervosaMussaenda benguetensisMussaenda multibracteataMussaenda pinatubensisMussaenda vidalii

Mussaenda philippicaMussaenda palawenensis

Pseudomussaendastenocarpa


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algae

algae

algae

moldsmolds

moldsalgaealgae

molds

algae

bryophytes

pteridophytes

gymnosperm

angiosperm


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Maximum Parsimony (MP)Parsimony:General scientific criterion for choosing amongcompeting hypotheses that states that we should

accept the hypothesis that explains the data mostsimply and efficiently.

States that the cladogram having the least number

of changes between characters is the best tree.

Find topology requiring smallest number ofevolutionary changes



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Sites 3 6 8

Tree I

Tree II

Tree III

T C A G A T C T A G

T T A G A A C T A G

T T C G A T C G A G

T T C T A A G G A C

OTU 1 2 3 4 5 6 7 8 9 10 Site

1

2

3

4

Choosing theshortest tree

with parsimony

1A 3C

2A 4C

Short Excercise:


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Sites 3 6 8

Tree I4 steps

best tree

Tree II

5 steps

Tree III6 steps

T C A G A T C T A G

T T A G A A C T A G

T T C G A T C G A G

T T C T A A G G A C

OTU 1 2 3 4 5 6 7 8 9 10 Site

1

2

3

4

Choosing the shortest

tree with parsimony

1A 3C

2A 4C

1T 3T

2A 4A

1T 3G

2T 4G

1A 2A

3C 4C

1T 2A

3T 4A

1T 2T

3G 4G

1A 2A

4C 3C

1T 2A

4A 3T

1T 2T

3G 4G

A C

AA

C C

AA

AT

T T

T G

T T

G G



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Taxa (n) rooted

(2n-3)!/(2n-2(n-2)!)

unrooted

(2n-5)!/(2n-3(n-3)!)

2 1 1

3 3 1

4 15 3

5 105 15

6 954 105

7 10,395 954

8 135,135 10,395

9 2,027,025 135,135

10 34,459,425 2,027,025

Phylogenetic Analysis Using Parsimony
http://paup.csit.fsu.edu/index.htmlhttp://paup.csit.fsu.edu/index.html


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Phylogenetic approach

2 ways Classic phylogeneticanalysis uses morphological

features

Ex: anatomy, size, shape, etc.

Modern phylogeneticanalysis uses molecularinformation

Genetic material (DNA and protein sequences)


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Sources of Systematic evidence

Morphology gross structure


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Anatomy tissues and cell types


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Physiology metabolic processes


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Embryology development


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Palynologypollen grains and their development


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Reproductive Biology e.g., pollination mechanism


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Molecular Systematics Genomic DNA sequences


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Phylogenetic approach

Types of Characters and Character states

Morphology:

Petal color

0 white

1 red

2 blue

Molecular:

260 * 280 * 300 * 3200841r : CCTTCAATTTTTATT-----------------------AGAGTTTTAGGAGAAATAAGTATGTG : 2720992r : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 2133803r : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 3054062r : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGAACAGAGTTTTAGGAGAAATAAGTATGTG : 3193802r : CCTCCAATTTTTATTAGTTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 282ph2f : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 306

CCTcCAATTTTTATTag ttgcctactcctttggg acAGAGTTTTAGGAGAAATAAGTATGTG


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Understanding Genome

Genome=Total genetic materials of an organism

Mitochondrial

Genome

Chloroplast

Genome

Nuclear

Genome

rbcL , atpB,

matK, ndhF,

rps16 intron,

atpB-rbcL intergenic region,

trn spacers (trnT, trnL, trnF),

16S rDNA

18S rDNA

26S rDNA

ITS

coxl

atpA


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Internal Transcribed Spacer (nrDNA)

(Baldwin et. al., 1995)

Gymnosperm: ITS1500 3700 bp

Angiosperm:ITS1 187-298 bp

5.8s163-165 bp

ITS2 187-252 bp


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(Taberlet et. al, 1991)

(Soltis at Soltis, 1998)

trnT-F (cpDNA)chloroplast genome



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Advantages of using molecular data

Why molecular data are powerful for evolutionarystudies?

They give more characters. Some organisms have limitednumber of morphological characters that can be used fortaxonomic purposes.

Molecular data are often easier to quantitate than aremorphological data.

DNA sequences more simple to model, only four characterstates A, C, G, T.

Molecular data have often resolved systematic questions wheremorphological evidence is inconlusive.

Molecular data have often revealed relationships that are not

suspected on the basis of traditional morphological characters

part 02 phylogenetics

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