Transcript
8/3/2019 Part 02 Phylogenetics
1/32
1
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. gdalejandro@mnl.ust.edu.ph
mailto:gdalejandro@mnl.ust.edu.phmailto:gdalejandro@mnl.ust.edu.ph8/3/2019 Part 02 Phylogenetics
2/32
2
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
8/3/2019 Part 02 Phylogenetics
3/32
3
Stuessy 1979:622
Systematics & Phylogenetic Revolution
8/3/2019 Part 02 Phylogenetics
4/32
4
Systematics & Phylogenetic Revolution
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%3DG8/3/2019 Part 02 Phylogenetics
5/32
5
Systematics & Phylogenetic Revolution
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
8/3/2019 Part 02 Phylogenetics
6/32
6
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
8/3/2019 Part 02 Phylogenetics
7/32
7
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
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
8/3/2019 Part 02 Phylogenetics
8/32
8
Phenetics vs Cladistics
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
8/3/2019 Part 02 Phylogenetics
9/32
9
Phylogenetic trees
Cladogram
8/3/2019 Part 02 Phylogenetics
10/32
10
Phylogenetic trees
8/3/2019 Part 02 Phylogenetics
11/32
11
Phylogenetic trees
8/3/2019 Part 02 Phylogenetics
12/32
12
Phylogenetic grouping
A monophyletic group includes the most recentcommon ancestor of the group and all of itsdescendants.
8/3/2019 Part 02 Phylogenetics
13/32
13
Phylogenetic grouping
A paraphyletic group includes the most recent
common ancestor of the group, but not all ofits descendants.
8/3/2019 Part 02 Phylogenetics
14/32
14
Phylogenetic grouping
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
8/3/2019 Part 02 Phylogenetics
15/32
15
algae
algae
algae
moldsmolds
moldsalgaealgae
molds
algae
bryophytes
pteridophytes
gymnosperm
angiosperm
8/3/2019 Part 02 Phylogenetics
16/32
16
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
Phylogenetic grouping
8/3/2019 Part 02 Phylogenetics
17/32
17
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:
8/3/2019 Part 02 Phylogenetics
18/32
18
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
Phylogenetic grouping
8/3/2019 Part 02 Phylogenetics
19/32
19
Phylogenetic grouping
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.html8/3/2019 Part 02 Phylogenetics
20/32
20
Phylogenetic approach
2 ways Classic phylogeneticanalysis uses morphological
features
Ex: anatomy, size, shape, etc.
Modern phylogeneticanalysis uses molecularinformation
Genetic material (DNA and protein sequences)
8/3/2019 Part 02 Phylogenetics
21/32
21
Sources of Systematic evidence
Morphology gross structure
8/3/2019 Part 02 Phylogenetics
22/32
22
Sources of Systematic evidence
Anatomy tissues and cell types
8/3/2019 Part 02 Phylogenetics
23/32
23
Sources of Systematic evidence
Physiology metabolic processes
8/3/2019 Part 02 Phylogenetics
24/32
24
Sources of Systematic evidence
Embryology development
8/3/2019 Part 02 Phylogenetics
25/32
25
Sources of Systematic evidence
Palynologypollen grains and their development
8/3/2019 Part 02 Phylogenetics
26/32
26
Sources of Systematic evidence
Reproductive Biology e.g., pollination mechanism
8/3/2019 Part 02 Phylogenetics
27/32
27
Sources of Systematic evidence
Molecular Systematics Genomic DNA sequences
8/3/2019 Part 02 Phylogenetics
28/32
28
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
8/3/2019 Part 02 Phylogenetics
29/32
29
Sources of molecular data
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
8/3/2019 Part 02 Phylogenetics
30/32
30
Sources of molecular data
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
8/3/2019 Part 02 Phylogenetics
31/32
31
(Taberlet et. al, 1991)
(Soltis at Soltis, 1998)
trnT-F (cpDNA)chloroplast genome
Sources of molecular data
8/3/2019 Part 02 Phylogenetics
32/32
32
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
top related