Phylogenetic Analysis – Part I

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Phylogenetic Analysis – Part I

Spring

2014

Outline

Systematics

Phenetics (brief review)

Phylogenetics & Characters

Evolutionary Trees

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.)

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.

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)

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 similarity

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 weight

Phenetics vs. Phylogenetics

Vertebrate limbs

A plant example:

cacti

euphorbs

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!

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…)

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.

Another example:

Character = leaf arrangement.

Character states = ???

Another example:

Character = leaf arrangement.

Character states

(depending on the group)

=

-alternate

-opposite

-whorled

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.

What is HOMOLOGY?

What is HOMOLOGY?

Similarity due to inheritance

of a feature from a common

ancestor; may be associated

with a change in function.

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’

a

Leaf modified as:

-pitcher for catching insects

-jaws for catching insects

-colored, petal-like bracts for attracting pollinators

-spines for protection

Characters

Homologous characters

example: perianth (petal & sepal) modification

An animal example

Forelimbs of human, cat, whale, bat

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)

Remember this?

Cacti (vegetative)

Euphorbs (vegetative)

cacti

euphorbs

Flowers and fruits show

that these are two groups

with different origins.

Characters

Homologous vs. Homoplasious

Similarity – includes detailed structure

Position

Development

Congruence – various types of evidence give

the same answer

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 identity

TIME

C

B

A

Evolutionary Trees

TIME

C

B

A

Stem shape

Petal number

Evolutionary Trees

C

B

A

Stem shape

Petal number

Evolutionary Trees

TIME

C

B

A

square stem

5 petals

Evolutionary Trees

Stem shape

Petal number

Terminology

Apomorphy

= derived character state

Plesiomorphy

= ancestral character state

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

apomorphic

?

Plesiomorphic

?

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

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.

Terminology

For our purposes:

an evolutionary tree = phylogeny =

cladogram

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

topology

.

Equivalent (Congruent) Cladograms

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

The

Same

Cladogram…

…these trees are topologically congruent.

Common Phylogenetic Tree Terminology

Clades or Branches or lineages

Terminal nodes

Ancestral node or root

Sister groups

Internal nodes or divergence points

Polytomy

(

plesiomorphic

)

(

apomorphic

)

Phylogenetic definitions of groups/taxa

Monophyletic

taxon – contains a common ancestor and

all

of its

descendents

A clade by definition is monophyletic!

Phylogenetic definition of groups/taxa

Paraphyletic

taxon – contains a common ancestor and some,

but not all

of its

descendents

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.

Phylogenetic definition of groups/taxa

Polyphyletic

taxon – a

composite taxon

derived from

2 or more ancestral sources

(taxa)

Examples of monophyly and paraphyly

Example of polyphyly

Traditional concept of plants included:

Green plants

Fungi

Blue-green algae

(cyanobacteria)

Euglenas

Red algae

Diatoms

Tree of Life Showing Groups Previously

Classified as Plants

(see Fig. 1.1 in Simpson)

Another way to think about it.

monophyletic

paraphyletic

polyphyletic

Source: Stuessy (1990)