Spring 2014 Outline Systematics Phenetics brief review Phylogenetics amp Characters Evolutionary Trees Systematics Science of organismal diversity Discovery description and interpretation of biological diversity ID: 540158
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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
PolytomySlide38Slide39
(
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)