Phylogenetic Analysis – Part I

Spring 2013

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. PhylogeneticsVertebrate 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.

CharactersHomologous 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

CharactersHomologous characters• example: perianth (petal & sepal) modification

An animal exampleForelimbs of human, cat, whale, bat

CharactersHomoplasious 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 showthat these are two groupswith different origins.

CharactersHomologous vs. Homoplasious

• Similarity – includes detailed structure• Position• Development• Congruence – various types of evidence give the same answer

CharactersHomologous characters

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

ABC model of floral organ identity

TIM

E

C B A

Evolutionary Trees

TIM

E

C B A

Stem shape Petal number

Evolutionary Trees

C B A

Stem shape

Petal number

Evolutionary Trees

TIM

E

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 petalsPlesiomorphic: 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.

TerminologyFor 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 lineagesTerminal nodesAncestral node or rootSister groupsInternal nodes or divergence pointsPolytomy

(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 describeall metazoans without a vertebral column—This is a group that does not include alldescendents 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 polyphylyTraditional 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)