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Phylogeny and the Tree of Life
Chapter 26
BCOR 012
February 12, 2010
Outline for February 12, 2010
Systematics: Connecting Classification to Phylogeny
Systematics, Taxonomy, and Phylogeny
Constructing cladograms
Phylogenetic Classification
Molecular Systematics
Parsimony
Systematics is the study of biological diversity
in an evolutionary context. It includes (among
other aspects) taxonomy, classification, and
phylogeny.
Taxonomy is the branch of systematics concerned
with naming and classification.
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• Scientific names are binomials
Carolus Linnaeus
• Example: Acer saccharum
1707-1778
- Acer is the genus name - it is a Latin noun
- saccharum is the specific epithet - it is a Latin
adjective
Classification
What are systems of classification intended to do?
(In other words, why do we bother with them?)
1. A system of classification is a helpful way to organize and
retrieve information.
Examples: the Library of Congress system for cataloging books;
the alphabetical telephone directory
2. A biological classification can allow you to make predictions
about the organisms being classified, but only if the system is based
on evolutionary relationship.
Example: Predictions about the possible medicinal properties of
plants are more likely to be accurate if those predictions are based on
knowledge of the medicinal properties of that plant’s near relatives.
Taxus brevifolia
Pacific yew
Biological
classifications are
hierarchical: each
taxonomic group is
nested within a
more inclusive
higher order group.
(Note that only the genus name
and specific epithet are italicized.)
From Two Kingdoms to Three Domains
• Early taxonomists classified all species as either
plants or animals
• Later, five kingdoms were recognized: Monera
(prokaryotes), Protista, Plantae, Fungi, and
Animalia
• More recently, the three domain system has
been adopted: Bacteria, Archaea, and Eukarya
EUKARYA
eukaryotes
Dinoflagellates
Forams
Ciliates Diatoms
Red algae
Land plants
Green algae
Cellular slime molds
Amoebas
Euglena
Trypanosomes
Leishmania
Animals
Fungi
Sulfolobus
Green nonsulfur bacteria
Thermophiles
Halophiles
(Mitochondrion)
COMMON
ANCESTOR
OF ALL
LIFE
Methanobacterium
ARCHAEA
both are prokaryotic
Spirochetes
Chlamydia
Green
sulfur bacteria
BACTERIA
Cyanobacteria
(Plastids, including
chloroplasts)
Phylogeny and Classification
“Our classifications
will come to be, as
far as they can be
so made, genealogies.”
- Charles Darwin, 1859
Phylogeny is the study of evolutionary relationships
among organisms.
Willi Hennig, 1913 - 1976
Founder of Phylogenetic
Systematics
(also called cladistics)
In phylogenetic analysis, taxa are associated on the
basis of shared evolutionary innovations.
One of the evolutionary
innovations shared by birds
is the feather …
A cladogram is an evolutionary hypothesis: it
summarizes information about ancestordescendent relationships.
Branch points represent an inferred
common ancestor. On the diagram,
the red star denotes the common
ancestor of leopard and turtle, while
the yellow star indicates the common
ancestor of tuna, salamander, turtle,
and leopard.
Q. Which of the following species pairs are most closely related?
A. Species 1 and 2
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B. Species 4 and 5
5
4
3
2
1
C. Species 3 and 4
Clicker Question
D. A and C are equivalently
correct
Phylogeny of five violet species
E. No two species are more
closely related to each other
than they are to the other
three
How to construct a cladogram:
•
•
•
•
•
Choose a study group
Choose an appropriate outgroup
Compile data matrix
Polarize characters
Use shared derived characters to associate
study group taxa and construct the
cladogram
The outgroup is the group used to polarize character
states in the study group. It should be the group
most closely related (on the basis of other lines of
evidence) to the study group that is not actually part
of the study group.
lancelet
Kinds of Characters
• Apomorphy - a derived character state
• Synapomorphy - a shared derived
character state
• Autapomorphy - a derived character state
unique to one study group member
Cladistic Analysis: Kinds of
Groups
A monophyletic group includes a common ancestor and
all of its descendents
Example: Reptilia (defined to include birds)
A paraphyletic group includes a common ancestor and some
but not all of its descendents
Example: Reptilia (defined to exclude birds)
A polyphyletic group is a group whose members do not share
a recent common ancestor
Example: homeotherms (warm-blooded animals)
Phylogenetic Classification, Rules of the Game:
In a phylogenetic classification, only
monophyletic groups are named.
If a paraphyletic group bears a name, it will
be an informal one (e.g., ‘gymnosperms’)
The nested relationship of clades is reflected in the
nested relationship of taxa in the resultant
classification.
It it critical to distinguish homology from analogy in phylogeny
reconstruction
Incorrect interpretation of the fourchambered heart as a homology
would lead to incorrect assessment
of the relationship of birds and
mammals.
Convergent evolution of stem succulence
in Euphorbiaceae and Cactaceae
The four-chambered heart evolved at least twice in
vertebrate history.
Molecular Phylogenetics
G
In molecular phylogenetic studies, individual nucleotide
positions are the characters, while the particular
nucleotide occurring at that position is the character
state.
Using parsimony analysis to choose among competing cladograms.
A
B
C
Under the principle of parsimony, tree A would be
preferred over B and C as it is one or two steps
shorter.
A cladogram is an evolutionary hypothesis.
It can be revised as new evidence becomes
available.
It’s rather remarkable,
wouldn’t you say?
Molecular systematics
is shedding new light
on the evolution of life on
earth.
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TIFF (Unc ompres sed) dec ompres sor
are needed to see this pic ture.