Phylogeny and the Tree of Life

Chapter 26
BCOR 012
February 4,7, 2011
 Outline for February 4,7 2011

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

•speciation
•taxonomy
•phylogeny.
Taxonomy is the branch of systematics concerned
with naming and classification.

• Scientific names are binomials

• Example: Acer saccharum Carolus Linnaeus
1707-1778
- Acer is the genus name - it is a Latin noun
- saccharum is the specific epithet - it is a Latin
adjective
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.)
Fig. 26-4
Order Family Genus Species

Panthera
Felidae
Pantherap
ardus

Taxidea
Carnivora

Taxidea

Mustelidae
taxus

Lutra
Lutra lutra

Canis
latrans
Canidae

Canis

Canis
lupus
 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 the
pattern of divergence history.

(as opposed to speciation, which

addresses process.)
Willi Hennig, 1913 - 1976
Assembling a phylogeny
Founder of Phylogenetic
using cladistics, taxa are Systematics
associated on the (also called cladistics)
basis of shared evolutionary
innovations.
One of the evolutionary
innovations shared by birds
is the feather …

Homology, the sharing of an innovation (derived

character) because of its invention in a common ancestor
Serial Homology of the Lobster
Figure 34.4b-c  Chordate segmentation
CRUSTACEANS COMPARED - EVOLUTIONARY HOMOLOGY
 CRUSTACEANS COMPARED:
EVOLUTIONARY TRANSFORMATION

ROCK CRAB
LOBSTER
Fig. 26-8
1

Deletion
2

Insertion

4
Fig. 26-8a

Deletion
2

Insertion
Fig. 26-8b

4
DNA Evolution: stable and labile characters relate to function.
Example: Homeobox genes, which govern variation in serial
homologs.
The homeobox (in the gene) codes for a homeodomain (in the
protein synthesized from the gene). The homeodomain has a
precise three-dimensional structure related to its function.

In evolution, the
homeodomain is
relatively stable
because it has a
precise job.
Amino acid
sequences
compared
for the
homeotic
gene Ubx
insects

arthropods

Dm - Fruitfly
Tc - Beetle
Jc - Butterfly
Ak - Onycho-
phoran
Decides six legs or more
Parsimony
Under the principle
of parsimony, tree A Ockham's razor.:
would be when trying to
preferred over B and choose between
C as it is one step multiple
shorter. competing theories
the simplest theory
is probably the
best.
 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
 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 primitive character is the one shared by the outgroup and
some, but not all, of the study group.
 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
 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
• Symplesiomorphy – a shared primitive
character state
 Cladistic Analysis and
Classification: 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)

 For Phylogenetic Classification, taxa
(taxonomic groups) should be natural groups,
that is groups reflecting phylogeny.

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. All are monophyletic groups.
 EUKARYA eukaryotes
Land plants Dinoflagellates
Green algae Forams
Ciliates Diatoms
Red algae

Amoebas
Cellular slime molds
Euglena
Trypanosomes
Animals
Leishmania
Fungi

Sulfolobus
Green nonsulfur bacteria
Thermophiles (Mitochondrion)

Spirochetes
Halophiles Chlamydia
COMMON
ANCESTOR Green
OF ALL sulfur bacteria
LIFE
Methanobacterium BACTERIA
Cyanobacteria
ARCHAEA both are prokaryotic (Plastids, including
chloroplasts)