Phylogenetic Analysis – Part I - PowerPoint Presentation

Slide1

Phylogenetic Analysis – Part I

Spring

2014Slide2

Outline

Systematics

Phenetics (brief review)

Phylogenetics & Characters

Evolutionary TreesSlide3

Systematics

Science of organismal diversity.

Discovery, description and interpretation of biological diversity.

Discovery and description of the evolutionary tree of life.

Synthesis of information in the form of predictive classification systems.

Production of identification tools (e.g., keys, floras and faunas, monographs, etc.)Slide4

Some important definitions

Systematics

= the study of the biological diversity on Earth and its evolutionary history.

Taxon

(pl.

taxa

) = a group of organisms distinct enough to be distinguished by a name and ranked in a definite category.

Classification

= the delimitation, ordering and ranking of taxa.

Taxonomy

= the theory and practice of classifying organisms.Slide5

Phylogenetics

Greek:

phylon

= tribe, race

genetikos

= refers to birth

(from

genesis

= birth)

= the study of the evolutionary relationships of organisms

Phylogeny

= evolutionary relationships;

genealogical (through time)Slide6

Phenetics:

Historically, systematists relied on similarities to classify organisms

Pheno = Greek for display, referring to visible characteristics

Phenetics

= method of classifying organisms based on overall similaritySlide7

Phenetic Classification Systems

Were originally designed to reflect God’s plan of creation [“natural order”]

Later systems were considered “natural” in that presumably related plants were grouped together.

Were based on many characters selected from experience, not from a pre-existing theory

Overall similarity was the main criterion; all characters had equal weightSlide8

Phenetics vs. Phylogenetics

Vertebrate limbsSlide9

A plant example:

cacti

euphorbsSlide10

Phenetics is

not

Sufficient….

Modern systematists seek an evolutionary interpretation for the relationships between organisms.

Simple “matching” or relationships based on superficial similarity may not reflect evolutionary relationships.

Testability and identification of specific characters used to group taxa is lacking in most phenetic methods.

Character-based, evolutionarily interpreted inter-taxon comparisons deemed superior! Slide11

Phylogenetics & Characters

Based on an explicit set of

a priori

assumptions on how the

characters

used have evolved. Relies heavily on evolutionary information.

Data are scored and analyzed following testable methods using shared derived character states to build evolutionary trees (phylogenies).

Methods are continually being developed that enhance the reliability of the analyses, and that provide tests for statistical support for the groups determined by the process. (More on this later…) Slide12

What is a character?

Character

= any feature of the organism, especially one with variation that helps to define groups. E.g., flower color.

Character state

= one of the various conditions or values of a character observed across a given group of taxa. E.g., red, white, pink, yellow are states for flower color.Slide13

Another example:

Character = leaf arrangement.

Character states = ???Slide14

Another example:

Character = leaf arrangement.

Character states

(depending on the group)

=

-alternate

-opposite

-whorledSlide15

Phylogenetic Analyses

Philosophy:

Determine relationships based upon

uniquely derived and shared character state changes

as evidence of common ancestry. Relies on the principle of homology.

Slide16

What is HOMOLOGY?

Slide17

What is HOMOLOGY?

Similarity due to inheritance

of a feature from a common

ancestor; may be associated

with a change in function.Slide18

Characters

Homologous characters (homology)

Character states of 2 or more taxa are homologous if the character is found in their common ancestor

2 character states (or features) are homologous if one is directly (or sequentially) derived from another

a

a

a

a’

aSlide19

Leaf modified as:

-pitcher for catching insects

-jaws for catching insects

-colored, petal-like bracts for attracting pollinators

-spines for protectionSlide20

Characters

Homologous characters

example: perianth (petal & sepal) modificationSlide21

An animal example

Forelimbs of human, cat, whale, batSlide22

Characters

Homoplasious characters (homoplasy)

Result of convergence, parallelisms, or reversals

Describes a character state found in 2 taxa if the common ancestor did not have this character or one character state is not the precursor of another (= superficial similarity)Slide23

Remember this?

Cacti (vegetative)

Euphorbs (vegetative)Slide24

cacti

euphorbs

Flowers and fruits show

that these are two groups

with different origins.Slide25

Characters

Homologous vs. Homoplasious

Similarity – includes detailed structure

Position

Development

Congruence – various types of evidence give

the same answerSlide26

Characters

Homologous characters

molecular evidence: genetic basis for homology (or not!) of basic features and how they have been modified

ABC model of floral organ identitySlide27

TIME

C

B

A

Evolutionary TreesSlide28

TIME

C

B

A

Stem shape

Petal number

Evolutionary TreesSlide29

C

B

A

Stem shape

Petal number

Evolutionary TreesSlide30

TIME

C

B

A

square stem

5 petals

Evolutionary Trees

Stem shape

Petal numberSlide31

Terminology

Apomorphy

= derived character state

Plesiomorphy

= ancestral character state

In the example we just looked at, which character states are

apomorphic

?

Plesiomorphic

?

Slide32

Terminology

Apomorphy

= derived character state

Plesiomorphy

= ancestral character state

In the example we just looked at, which character states are

apomorphic

?

Plesiomorphic

?

Apomorphic

: square stems, 5 petals

Plesiomorphic

: round stems, 4 petals

Slide33

Terminology

Synapomorphy

– shared derived character for two or more taxa or lineages; defines clades.

Symplesiomorphy

– shared ancestral (

underived

) character – uninformative.

Autapomorphy

– derived character state occurring in only ONE taxon – uninformative.

Clade

– group of taxa defined by at least one

synapomorphy

; branch of an evolutionary tree; a lineage.

Slide34

Terminology

For our purposes:

an evolutionary tree = phylogeny =

cladogram

The shape of the tree (the branching order) is known as the

topology

.

Slide35

Equivalent (Congruent) Cladograms

Cladograms 1, 2, and 3 have the same topology.Slide36

The

Same

Cladogram…

…these trees are topologically congruent.Slide37

Common Phylogenetic Tree Terminology

Clades or Branches or lineages

Terminal nodes

Ancestral node or root

Sister groups

Internal nodes or divergence points

PolytomySlide38
Slide39

(

plesiomorphic

)

(

apomorphic

)Slide40

Phylogenetic definitions of groups/taxa

Monophyletic

taxon – contains a common ancestor and

all

of its

descendentsSlide41

A clade by definition is monophyletic!Slide42

Phylogenetic definition of groups/taxa

Paraphyletic

taxon – contains a common ancestor and some,

but not all

of its

descendentsSlide43

Example of Paraphyly

The term “invertebrate” is used to describe

all metazoans without a vertebral column—

This is a group that does not include all

descendents of animals.Slide44

Phylogenetic definition of groups/taxa

Polyphyletic

taxon – a

composite taxon

derived from

2 or more ancestral sources

(taxa)Slide45

Examples of monophyly and paraphylySlide46

Example of polyphyly

Traditional concept of plants included:

Green plants

Fungi

Blue-green algae

(cyanobacteria)

Euglenas

Red algae

DiatomsSlide47

Tree of Life Showing Groups Previously

Classified as Plants

(see Fig. 1.1 in Simpson)Slide48

Another way to think about it.

monophyletic

paraphyletic

polyphyletic

Source: Stuessy (1990)