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
Evolutionary Trees
TIME
C
B
A
Evolutionary Trees
B
A
TIME
C
Stem shape
Petal number
Evolutionary Trees
C
B
A
Petal number
Stem shape
Evolutionary Trees
C
B
A
TIME
5 petals
square stem
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
(apomorphic)
(plesiomorphic)
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)
Red algae
Euglenas
Diatoms
Tree of Life Showing Groups Previously
Classified as Plants
(see Fig. 1.1 in Simpson)
Another way to think about it.
monophyletic
Source: Stuessy (1990)
paraphyletic
polyphyletic