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

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 using molecular data

Basic Methods in Phylogenetics

Systematics & Phylogenetic Revolution

Stuessy 1979:622
3

Systematics & Phylogenetic Revolution

Phylogenetic systematics - reconstruction and study of evolutionary relationships. Evolutionary theory similarity among species is due to a common descent, or inheritance from a common ancestor. Phylogeny - the historical relationships among lineages or organisms, such as their genes.
Willi Hennig (German entomologist, 1950s) proposed that systematics should reflect the known evolutionary history of lineages as closely as possible, an approach he called phylogenetic systematics.

Systematics & Phylogenetic Revolution

Phylogenetics = Cladistics The followers of Hennig were disparingly referred to as "cladists" by his opponents, because of the emphasis on recognizing only monophyletic groups, a group plus all of its descendents, or clades. However, the cladists quickly adopted that term as a helpful label, and nowadays, cladistic approaches to systematics are used routinely.

Phenetics vs Cladistics
Phenetic (overall similarity)

characteristics critter A 4 limbs meta. hair kidney critter B 4 limbs meta. hair kidney critter C 4 limbs meta. feathers kidney endothermy vivip. no cloaca endothermy ovip. endothermy ovip. ovip.
B

identity placental echidna bird turtle

A

cloaca cloaca cloaca

ancestor 4 limbs meta. no ectothermy kidney hair/feathers

4
B 5 C
6

3
overall similarity

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

characteristics critter A 4 limbs meta. hair kidney critter B 4 limbs meta. hair kidney critter C 4 limbs meta. feathers kidney endothermy vivip. no cloaca endothermy ovip. endothermy ovip. ovip. cloaca cloaca cloaca

identity placental echidna bird turtle

ancestor 4 limbs meta. no ectothermy kidney hair/feathers

A 2 B 1 C
7

shared derived characters (synapomorphy)

Phenetics vs Cladistics
Characters 1 2 Species A B C 0 1 1 0 1 0 3 0 0 1 4 0 0 1 5 0 0 1

Phenetic
Overall similarities A A B C B .60 C .20 .20 -

Cladistic
0 = Primitive character state or plesiomorphic 1 = Derived character state Character 1 = shared derived or synapomorphic Character 2 = uniquely derived or autopomorphic

Similarity % 100 80 60 40 20 0

Character 1
8

Phylogenetic trees

Cladogram

Phylogenetic trees

10

Phylogenetic trees

11

Phylogenetic grouping

A monophyletic group includes the most recent common ancestor of the group and all of its descendants.

12

Phylogenetic grouping

A paraphyletic group includes the most recent common ancestor of the group, but not all of its descendants.

13

Phylogenetic grouping

A polyphyletic group does not include the most recent common ancestor of all the members.

Sabicea diversifolia Warszewiczia coccinea Heinsia crinita Heinsia zanzibarica Heinsia bussei Landiopsis capuronii Mussaenda sp. nov. Mussaenda pervillei Mussaenda latisepala Mussaenda erectiloba Mussaenda vestita Pseudomussaenda rivularis Pseudomussaenda stenocarpa Pseudomussaenda flava Pseudomussaenda stenocarpa Mussaenda arcuata Mussaenda monticola Mussaenda nivea Mussaenda erythrophylla Mussaenda elegans Mussaenda grandiflora Mussaenda isertiana Mussaenda afzelii Mussaenda pubescens Mussaenda shikokiana Mussaenda parvifolia Mussaenda uniflora Mussaenda uniflora Mussaenda uniflora Mussaenda reinwardtiana Mussaenda nervosa Mussaenda benguetensis Mussaenda multibracteata Mussaenda pinatubensis Mussaenda vidalii 14 Mussaenda philippica Mussaenda palawenensis

algae molds molds algae algae molds algae algae molds algae

bryophytes
pteridophytes gymnosperm angiosperm
15

Phylogenetic grouping

Maximum Parsimony (MP)

Parsimony: General scientific criterion for choosing among competing hypotheses that states that we should accept the hypothesis that explains the data most simply and efficiently. States that the cladogram having the least number of changes between characters is the best tree. Find topology requiring smallest number of evolutionary changes

16

Short Excercise:

Choosing the shortest tree with parsimony

Sites
1A

OTU 1 2 3 4

1 T T T T

2 C T T T

3 A A C C

4 G G G T

5 A A A A

6 T A T A

7 C C C G

8 T T G G

9 A A A A

10 Site G G G C

3
3C 4C

Tree I
2A

Tree II

Tree III

17

Phylogenetic grouping

Choosing the shortest tree with parsimony

Sites
1A

OTU 1 2 3 4

1 T T T T

2 C T T T

3 A A C C

4 G G G T

5 A A A A

6 T A T A

7 C C C G

8 T T G G

9 A A A A

10 Site G G G C

3
3C A 2A 1A C 4C 2A A 3C 1A C 4C C 3C 4A A 4C 2A 3T 1T T 2A 1T A

6
3T A 4A 2T 1T

8
3G

Tree I
4 steps best tree

G
4G

1T
T A

2A
4A 2A T 3T

1T
T 3G 1T G 3G G T

2T
4G 2T 4G
18

Tree II
5 steps

Tree III
6 steps

Phylogenetic grouping

Taxa (n)

rooted (2n-3)!/(2n-2(n-2)!) 1 3 15 105

unrooted (2n-5)!/(2n-3(n-3)!) 1 1 3 15

2 3 4 5

6
7 8 9 10

954
10,395 135,135 2,027,025 34,459,425

105
954 10,395 135,135 2,027,025

Phylogenetic Analysis Using Parsimony

19

Phylogenetic approach

2 ways Classic phylogenetic analysis uses morphological features Ex: anatomy, size, shape, etc.

Modern phylogenetic analysis uses molecular information Genetic material (DNA and protein sequences)

20

Sources of Systematic evidence

Morphology gross structure

21

Sources of Systematic evidence

Anatomy tissues and cell types

22

Sources of Systematic evidence

Physiology metabolic processes

23

Sources of Systematic evidence

Embryology development

24

Sources of Systematic evidence

Palynology pollen grains and their development

25

Sources of Systematic evidence

Reproductive Biology e.g., pollination mechanism

26

Sources of Systematic evidence

Molecular Systematics Genomic DNA sequences

27

Phylogenetic approach

Types of Characters and Character states Morphology: Petal color 0 white 1 red 2 blue Molecular:
260 * 280 * 300 * 320 CCTTCAATTTTTATT-----------------------AGAGTTTTAGGAGAAATAAGTATGTG CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGAACAGAGTTTTAGGAGAAATAAGTATGTG CCTCCAATTTTTATTAGTTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG CCTcCAATTTTTATTag ttgcctactcctttggg acAGAGTTTTAGGAGAAATAAGTATGTG

0841r 0992r 3803r 4062r 3802r ph2f

: : : : : :

: : : : : :

272 213 305 319 282 306

28

Sources of molecular data

Understanding Genome

Genome = Total genetic materials of an organism

Mitochondrial Genome
coxl atpA

Chloroplast Genome
rbcL , atpB,

Nuclear Genome
18S rDNA
26S rDNA ITS

matK, ndhF,
rps16 intron, atpB-rbcL intergenic region, trn spacers (trnT, trnL, trnF), 16S rDNA

29

Sources of molecular data

Internal Transcribed Spacer (nrDNA)

(Baldwin et. al., 1995)

Gymnosperm: ITS 1500 3700 bp Angiosperm: ITS1 187-298 bp 5.8s 163-165 bp ITS2 187-252 bp
30

Sources of molecular data

chloroplast genome trnT-F (cpDNA)

(Taberlet et. al, 1991) (Soltis at Soltis, 1998)

31

Advantages of using molecular data

Why molecular data are powerful for evolutionary studies?

They give more characters. Some organisms have limited

number of morphological characters that can be used for taxonomic purposes.

Molecular data are often easier to quantitate than are

morphological data.

DNA sequences more simple to model, only four character

states A, C, G, T.

Molecular data have often resolved systematic questions where

morphological evidence is inconlusive.

Molecular data have often revealed relationships that are not

32 suspected on the basis of traditional morphological characters.